This document guides through the analysis of the MS data for the PTex HEK293 project. Inputdata have to be provided in the folder inputdata
inside the working directory. These are:
working directory/
PTex.Rmd
inputdata/
proteinGroups.txt # MS data
RBP table-Table 1.csv # Gerstberger review (2014) RBPs
human TFs-Table 1.csv # Gerstberger review (2014) TFs
2015-06-09_human_interactomes.csv # Landthaler human mRNA IC
preiss_genenames.csv # Preiss
Brannan_annotated.txt # Brannan SONAR annotated RBPs
Brannan_SONAR_0.79.txt # Brannan SONAR predicted
hubstenberger.csv # Hubstenberger P-Body Proteins
RICK_high_conf.csv # RICK high confidence
RICK_low_conf.csv # RICK low confidence
RICK_unique.csv # RICK unique
caric.csv # CARIC
human_proteome_reviewed_290118.list # UniProt SwissProt
UP000005640_9606_all.fasta.pI.csv # Isoelectricpointdb
The following libraries are needed for the analysis. Packages have to be installed prior to loading.
library("dplyr")
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
library("limma")
library("reshape2")
library("ggplot2")
library("GGally")
Attaching package: ‘GGally’
The following object is masked from ‘package:dplyr’:
nasa
library("Peptides")
library("DT")
To produce pairwise scatter plots with correlation information we use the ggpairs()
function from the GGally
package. Custom theme for pairwise scatter plots:
scatter_theme <- theme(legend.position = "none",
panel.grid.major = element_blank(),
axis.ticks = element_blank(),
panel.border = element_rect(linetype = "solid", colour = "black", fill = NA))
ggplot <- function(...) ggplot2::ggplot(...) + scale_colour_manual(values = c("black","red")) + scale_fill_manual(values = c("black","red"))
unlockBinding("ggplot",parent.env(asNamespace("GGally")))
assign("ggplot",ggplot,parent.env(asNamespace("GGally")))
The primary MS data are contained in the file proteinGroups.txt
.
primaryMassSpecData <- read.table("inputdata/proteinGroups.txt", header = TRUE, sep = "\t")
To ease later analyses, character vectors of columnnames are created.
intensities <- c("Intensity.Input_NoCl_I",
"Intensity.Input_NoCl_II",
"Intensity.Input_NoCl_III",
"Intensity.Input_0015_I",
"Intensity.Input_0015_II",
"Intensity.Input_0015_III",
"Intensity.Input_015_I",
"Intensity.Input_015_II",
"Intensity.Input_015_III",
"Intensity.Input_15_I",
"Intensity.Input_15_II",
"Intensity.Input_15_III",
"Intensity.PTex_NoCl_I",
"Intensity.PTex_NoCl_II",
"Intensity.PTex_NoCl_III",
"Intensity.PTex_0015_I",
"Intensity.PTex_0015_II",
"Intensity.PTex_0015_III",
"Intensity.PTex_015_I",
"Intensity.PTex_015_II",
"Intensity.PTex_015_III",
"Intensity.PTex_15_I",
"Intensity.PTex_15_II",
"Intensity.PTex_15_III")
LFQ <- c("LFQ.intensity.Input_NoCl_I",
"LFQ.intensity.Input_NoCl_II",
"LFQ.intensity.Input_NoCl_III",
"LFQ.intensity.Input_0015_I",
"LFQ.intensity.Input_0015_II",
"LFQ.intensity.Input_0015_III",
"LFQ.intensity.Input_015_I",
"LFQ.intensity.Input_015_II",
"LFQ.intensity.Input_015_III",
"LFQ.intensity.Input_15_I",
"LFQ.intensity.Input_15_II",
"LFQ.intensity.Input_15_III",
"LFQ.intensity.PTex_NoCl_I",
"LFQ.intensity.PTex_NoCl_II",
"LFQ.intensity.PTex_NoCl_III",
"LFQ.intensity.PTex_0015_I",
"LFQ.intensity.PTex_0015_II",
"LFQ.intensity.PTex_0015_III",
"LFQ.intensity.PTex_015_I",
"LFQ.intensity.PTex_015_II",
"LFQ.intensity.PTex_015_III",
"LFQ.intensity.PTex_15_I",
"LFQ.intensity.PTex_15_II",
"LFQ.intensity.PTex_15_III")
IBAQ <- c("iBAQ.Input_NoCl_I",
"iBAQ.Input_NoCl_II",
"iBAQ.Input_NoCl_III",
"iBAQ.Input_0015_I",
"iBAQ.Input_0015_II",
"iBAQ.Input_0015_III",
"iBAQ.Input_015_I",
"iBAQ.Input_015_II",
"iBAQ.Input_015_III",
"iBAQ.Input_15_I",
"iBAQ.Input_15_II",
"iBAQ.Input_15_III",
"iBAQ.PTex_NoCl_I",
"iBAQ.PTex_NoCl_II",
"iBAQ.PTex_NoCl_III",
"iBAQ.PTex_0015_I",
"iBAQ.PTex_0015_II",
"iBAQ.PTex_0015_III",
"iBAQ.PTex_015_I",
"iBAQ.PTex_015_II",
"iBAQ.PTex_015_III",
"iBAQ.PTex_15_I",
"iBAQ.PTex_15_II",
"iBAQ.PTex_15_III")
In a first filtering step reverse and hits only identified by site are removed.
MassSpecData <- primaryMassSpecData[primaryMassSpecData$Reverse != "+",]
MassSpecData <- MassSpecData[MassSpecData$Only.identified.by.site != "+",]
All intensites are log2 transformed.
MassSpecData[c(intensities, IBAQ, LFQ)] <- log2(MassSpecData[c(intensities, IBAQ, LFQ)])
Infinity values that resulted from log2 transformation are converted to NA
:
is.na(MassSpecData[c(intensities,IBAQ,LFQ)]) <- sapply(MassSpecData[c(intensities,IBAQ,LFQ)], is.infinite)
The LFQ intensities are normalised under the assumption that most intensities won’t change. This is not true for PTex data, so that the normalisation has to be corrected. Correction is done by using trypsin (added to all samples in the same amount) to calculate a normalisation factor.
trypsin = MassSpecData[MassSpecData$Majority.protein.IDs == "CON__P00761",]
trp_mean_Inp_NoCl <- mean(trypsin[,LFQ[1]],trypsin[,LFQ[2]],trypsin[,LFQ[3]])
trp_mean_Inp_0015 <- mean(trypsin[,LFQ[4]],trypsin[,LFQ[5]],trypsin[,LFQ[6]])
trp_mean_Inp_015 <- mean(trypsin[,LFQ[7]],trypsin[,LFQ[8]],trypsin[,LFQ[9]])
trp_mean_Inp_15 <- mean(trypsin[,LFQ[10]],trypsin[,LFQ[11]],trypsin[,LFQ[12]])
trp_mean_PTex_NoCl <- mean(trypsin[,LFQ[13]],trypsin[,LFQ[14]],trypsin[,LFQ[15]])
trp_mean_PTex_0015 <- mean(trypsin[,LFQ[16]],trypsin[,LFQ[17]],trypsin[,LFQ[18]])
trp_mean_PTex_015 <- mean(trypsin[,LFQ[19]],trypsin[,LFQ[20]],trypsin[,LFQ[21]])
trp_mean_PTex_15 <- mean(trypsin[,LFQ[22]],trypsin[,LFQ[23]],trypsin[,LFQ[24]])
nf_NoCl <- trp_mean_PTex_NoCl - trp_mean_Inp_NoCl
nf_0015Cl <- trp_mean_PTex_0015 - trp_mean_Inp_0015
nf_015Cl <- trp_mean_PTex_015 - trp_mean_Inp_015
nf_15Cl <- trp_mean_PTex_15 - trp_mean_Inp_15
Tidy up:
rm(list = ls(pattern = "trp_mean_"))
rm(trypsin)
After calculation of the normalisation factors the contaminants are removed from the data set.
MassSpecData <- MassSpecData[MassSpecData$Potential.contaminant != "+",]
The normalisation factors are applied by subtraction, since the data were already log transformed.
norm_MassSpecData <- MassSpecData
norm_MassSpecData[LFQ[13:15]] <- norm_MassSpecData[LFQ[13:15]] - nf_NoCl
norm_MassSpecData[LFQ[16:18]] <- norm_MassSpecData[LFQ[16:18]] - nf_0015Cl
norm_MassSpecData[LFQ[19:21]] <- norm_MassSpecData[LFQ[19:21]] - nf_015Cl
norm_MassSpecData[LFQ[22:24]] <- norm_MassSpecData[LFQ[22:24]] - nf_15Cl
Tidy up:
rm(list = ls(pattern = "nf_"))
We only want to consider those proteins, that were found in all replicates of all experiments.
for(exp in c("PTex_noCL","PTex_0015","PTex_015","PTex_15", "Input_noCL","Input_0015","Input_015","Input_15")){
sub_MassSpecData <- select(norm_MassSpecData, matches(paste("LFQ.intensity", exp, sep = ".")))
x <- apply(sub_MassSpecData, 1, function(x)sum(!is.na(x))>2)
norm_MassSpecData <- norm_MassSpecData[x,]
}
Tidy up:
rm(list = ls(pattern = "sub_"))
rm(exp)
rm(x)
## Input noCL
input_nocl_scatter <- ggpairs(norm_MassSpecData[,LFQ[1:3]],
lower = list(continuous = wrap("cor", size = 7)),
upper = list(continuous = "smooth"),
diag = list(continuous = "densityDiag")) + scatter_theme
## Input 0.015
input_0015_scatter <- ggpairs(norm_MassSpecData[,LFQ[4:6]],
lower = list(continuous = wrap("cor", size = 7)),
upper = list(continuous = "smooth"),
diag = list(continuous = "densityDiag")) + scatter_theme
## Input 0.15
input_015_scatter <- ggpairs(norm_MassSpecData[,LFQ[7:9]],
lower = list(continuous = wrap("cor", size = 7)),
upper = list(continuous = "smooth"),
diag = list(continuous = "densityDiag")) + scatter_theme
## Input 1.5
input_15_scatter <- ggpairs(norm_MassSpecData[,LFQ[10:12]],
lower = list(continuous = wrap("cor", size = 7)),
upper = list(continuous = "smooth"),
diag = list(continuous = "densityDiag")) + scatter_theme
## PTex noCL
ptex_nocl_scatter <- ggpairs(norm_MassSpecData[,LFQ[13:15]],
lower = list(continuous = wrap("cor", size = 7)),
upper = list(continuous = "smooth"),
diag = list(continuous = "densityDiag")) + scatter_theme
## PTex 0.015
ptex_0015_scatter <- ggpairs(norm_MassSpecData[,LFQ[16:18]],
lower = list(continuous = wrap("cor", size = 7)),
upper = list(continuous = "smooth"),
diag = list(continuous = "densityDiag")) + scatter_theme
## PTex 0.15
ptex_015_scatter <- ggpairs(norm_MassSpecData[,LFQ[19:21]],
lower = list(continuous = wrap("cor", size = 7)),
upper = list(continuous = "smooth"),
diag = list(continuous = "densityDiag")) + scatter_theme
## PTex 1.5
ptex_15_scatter <- ggpairs(norm_MassSpecData[,LFQ[22:24]],
lower = list(continuous = wrap("cor", size = 7)),
upper = list(continuous = "smooth"),
diag = list(continuous = "densityDiag")) + scatter_theme
input_nocl_scatter
input_0015_scatter
input_015_scatter
input_15_scatter
ptex_nocl_scatter
ptex_0015_scatter
ptex_015_scatter
ptex_15_scatter
Tidy up:
rm(list = ls(pattern = "_scatter"))
After preparation the fold changes between respective Input/PTex pairs can be calculated and a moderated t-test with following Benjamini-Hochberg correction is used to determine the false discovery rate (FDR).
The fold changes are calculated by subtracting the log-transformed LFQ intensity values of the non-crosslinked (-CL) from the crosslinked (+CL) samples.
norm_MassSpecData$FC.Input_0015.rep1 <- (norm_MassSpecData$LFQ.intensity.Input_0015_I - norm_MassSpecData$LFQ.intensity.Input_NoCl_I)
norm_MassSpecData$FC.Input_0015.rep2 <- (norm_MassSpecData$LFQ.intensity.Input_0015_II - norm_MassSpecData$LFQ.intensity.Input_NoCl_II)
norm_MassSpecData$FC.Input_0015.rep3 <- (norm_MassSpecData$LFQ.intensity.Input_0015_III - norm_MassSpecData$LFQ.intensity.Input_NoCl_III)
norm_MassSpecData$FC.Input_015.rep1 <- (norm_MassSpecData$LFQ.intensity.Input_015_I - norm_MassSpecData$LFQ.intensity.Input_NoCl_I)
norm_MassSpecData$FC.Input_015.rep2 <- (norm_MassSpecData$LFQ.intensity.Input_015_II - norm_MassSpecData$LFQ.intensity.Input_NoCl_II)
norm_MassSpecData$FC.Input_015.rep3 <- (norm_MassSpecData$LFQ.intensity.Input_015_III - norm_MassSpecData$LFQ.intensity.Input_NoCl_III)
norm_MassSpecData$FC.Input_15.rep1 <- (norm_MassSpecData$LFQ.intensity.Input_15_I - norm_MassSpecData$LFQ.intensity.Input_NoCl_I)
norm_MassSpecData$FC.Input_15.rep2 <- (norm_MassSpecData$LFQ.intensity.Input_15_II - norm_MassSpecData$LFQ.intensity.Input_NoCl_II)
norm_MassSpecData$FC.Input_15.rep3 <- (norm_MassSpecData$LFQ.intensity.Input_15_III - norm_MassSpecData$LFQ.intensity.Input_NoCl_III)
norm_MassSpecData$FC.PTex_0015.rep1 <- (norm_MassSpecData$LFQ.intensity.PTex_0015_I - norm_MassSpecData$LFQ.intensity.PTex_NoCl_I)
norm_MassSpecData$FC.PTex_0015.rep2 <- (norm_MassSpecData$LFQ.intensity.PTex_0015_II - norm_MassSpecData$LFQ.intensity.PTex_NoCl_II)
norm_MassSpecData$FC.PTex_0015.rep3 <- (norm_MassSpecData$LFQ.intensity.PTex_0015_III - norm_MassSpecData$LFQ.intensity.PTex_NoCl_III)
norm_MassSpecData$FC.PTex_015.rep1 <- (norm_MassSpecData$LFQ.intensity.PTex_015_I - norm_MassSpecData$LFQ.intensity.PTex_NoCl_I)
norm_MassSpecData$FC.PTex_015.rep2 <- (norm_MassSpecData$LFQ.intensity.PTex_015_II - norm_MassSpecData$LFQ.intensity.PTex_NoCl_II)
norm_MassSpecData$FC.PTex_015.rep3 <- (norm_MassSpecData$LFQ.intensity.PTex_015_III - norm_MassSpecData$LFQ.intensity.PTex_NoCl_III)
norm_MassSpecData$FC.PTex_15.rep1 <- (norm_MassSpecData$LFQ.intensity.PTex_15_I - norm_MassSpecData$LFQ.intensity.PTex_NoCl_I)
norm_MassSpecData$FC.PTex_15.rep2 <- (norm_MassSpecData$LFQ.intensity.PTex_15_II - norm_MassSpecData$LFQ.intensity.PTex_NoCl_II)
norm_MassSpecData$FC.PTex_15.rep3 <- (norm_MassSpecData$LFQ.intensity.PTex_15_III - norm_MassSpecData$LFQ.intensity.PTex_NoCl_III)
Mean fold changes are calculated.
norm_MassSpecData$FC.Input_0015.mean <- rowMeans(norm_MassSpecData[,251:253])
norm_MassSpecData$FC.Input_015.mean <- rowMeans(norm_MassSpecData[,254:256])
norm_MassSpecData$FC.Input_15.mean <- rowMeans(norm_MassSpecData[,257:259])
norm_MassSpecData$FC.PTex_0015.mean <- rowMeans(norm_MassSpecData[,260:262])
norm_MassSpecData$FC.PTex_015.mean <- rowMeans(norm_MassSpecData[,263:265])
norm_MassSpecData$FC.PTex_15.mean <- rowMeans(norm_MassSpecData[,266:268])
A moderated t-test including Benjamini-Hochberg p-value correction is layed out on the fold changes.
pval = eBayes(lmFit(norm_MassSpecData[,grep("FC.Input_0015.rep",names(norm_MassSpecData))]))
norm_MassSpecData$pval.Input_0015 <- pval$p.value
norm_MassSpecData$padj.Input_0015 <- p.adjust(norm_MassSpecData$pval.Input_0015, method="BH")
pval = eBayes(lmFit(norm_MassSpecData[,grep("FC.Input_015.rep",names(norm_MassSpecData))]))
norm_MassSpecData$pval.Input_015 <- pval$p.value
norm_MassSpecData$padj.Input_015 <- p.adjust(norm_MassSpecData$pval.Input_015, method="BH")
pval = eBayes(lmFit(norm_MassSpecData[,grep("FC.Input_15.rep",names(norm_MassSpecData))]))
norm_MassSpecData$pval.Input_15 <- pval$p.value
norm_MassSpecData$padj.Input_15 <- p.adjust(norm_MassSpecData$pval.Input_15, method="BH")
pval = eBayes(lmFit(norm_MassSpecData[,grep("FC.PTex_0015.rep",names(norm_MassSpecData))]))
norm_MassSpecData$pval.PTex_0015 <- pval$p.value
norm_MassSpecData$padj.PTex_0015 <- p.adjust(norm_MassSpecData$pval.PTex_0015, method="BH")
pval = eBayes(lmFit(norm_MassSpecData[,grep("FC.PTex_015.rep",names(norm_MassSpecData))]))
norm_MassSpecData$pval.PTex_015 <- pval$p.value
norm_MassSpecData$padj.PTex_015 <- p.adjust(norm_MassSpecData$pval.PTex_015, method="BH")
pval = eBayes(lmFit(norm_MassSpecData[,grep("FC.PTex_15.rep",names(norm_MassSpecData))]))
norm_MassSpecData$pval.PTex_15 <- pval$p.value
norm_MassSpecData$padj.PTex_15 <- p.adjust(norm_MassSpecData$pval.PTex_15, method="BH")
Tidy up:
rm(pval)
Mean intensities (LFQ and iBAQ) are calculated.
### LFQ
norm_MassSpecData$LFQ.intensity.Input_noCl_mean <- rowMeans(norm_MassSpecData[,c("LFQ.intensity.Input_NoCl_I", "LFQ.intensity.Input_NoCl_II", "LFQ.intensity.Input_NoCl_III")], na.rm = FALSE)
norm_MassSpecData$LFQ.intensity.Input_0015_mean <- rowMeans(norm_MassSpecData[,c("LFQ.intensity.Input_0015_I", "LFQ.intensity.Input_0015_II", "LFQ.intensity.Input_0015_III")], na.rm = FALSE)
norm_MassSpecData$LFQ.intensity.Input_015_mean <- rowMeans(norm_MassSpecData[,c("LFQ.intensity.Input_015_I", "LFQ.intensity.Input_015_II", "LFQ.intensity.Input_015_III")], na.rm = FALSE)
norm_MassSpecData$LFQ.intensity.Input_15_mean <- rowMeans(norm_MassSpecData[,c("LFQ.intensity.Input_15_I", "LFQ.intensity.Input_15_II", "LFQ.intensity.Input_15_III")], na.rm = FALSE)
norm_MassSpecData$LFQ.intensity.PTex_noCl_mean <- rowMeans(norm_MassSpecData[,c("LFQ.intensity.PTex_NoCl_I", "LFQ.intensity.PTex_NoCl_II", "LFQ.intensity.PTex_NoCl_III")], na.rm = FALSE)
norm_MassSpecData$LFQ.intensity.PTex_0015_mean <- rowMeans(norm_MassSpecData[,c("LFQ.intensity.PTex_0015_I", "LFQ.intensity.PTex_0015_II", "LFQ.intensity.PTex_0015_III")], na.rm = FALSE)
norm_MassSpecData$LFQ.intensity.PTex_015_mean <- rowMeans(norm_MassSpecData[,c("LFQ.intensity.PTex_015_I", "LFQ.intensity.PTex_015_II", "LFQ.intensity.PTex_015_III")], na.rm = FALSE)
norm_MassSpecData$LFQ.intensity.PTex_15_mean <- rowMeans(norm_MassSpecData[,c("LFQ.intensity.PTex_15_I", "LFQ.intensity.PTex_15_II", "LFQ.intensity.PTex_15_III")], na.rm = FALSE)
### iBAQ
norm_MassSpecData$iBAQ.Input_noCl_mean <- rowMeans(norm_MassSpecData[,c("iBAQ.Input_NoCl_I", "iBAQ.Input_NoCl_II", "iBAQ.Input_NoCl_III")], na.rm = FALSE)
norm_MassSpecData$iBAQ.Input_0015_mean <- rowMeans(norm_MassSpecData[,c("iBAQ.Input_0015_I", "iBAQ.Input_0015_II", "iBAQ.Input_0015_III")], na.rm = FALSE)
norm_MassSpecData$iBAQ.Input_015_mean <- rowMeans(norm_MassSpecData[,c("iBAQ.Input_015_I", "iBAQ.Input_015_II", "iBAQ.Input_015_III")], na.rm = FALSE)
norm_MassSpecData$iBAQ.Input_15_mean <- rowMeans(norm_MassSpecData[,c("iBAQ.Input_15_I", "iBAQ.Input_15_II", "iBAQ.Input_15_III")], na.rm = FALSE)
norm_MassSpecData$iBAQ.PTex_noCl_mean <- rowMeans(norm_MassSpecData[,c("iBAQ.PTex_NoCl_I", "iBAQ.PTex_NoCl_II", "iBAQ.PTex_NoCl_III")], na.rm = FALSE)
norm_MassSpecData$iBAQ.PTex_0015_mean <- rowMeans(norm_MassSpecData[,c("iBAQ.PTex_0015_I", "iBAQ.PTex_0015_II", "iBAQ.PTex_0015_III")], na.rm = FALSE)
norm_MassSpecData$iBAQ.PTex_015_mean <- rowMeans(norm_MassSpecData[,c("iBAQ.PTex_015_I", "iBAQ.PTex_015_II", "iBAQ.PTex_015_III")], na.rm = FALSE)
norm_MassSpecData$iBAQ.PTex_15_mean <- rowMeans(norm_MassSpecData[,c("iBAQ.PTex_15_I", "iBAQ.PTex_15_II", "iBAQ.PTex_15_III")], na.rm = FALSE)
We want to additionally exclude proteins that are not significantly enriched in all 3 libraries and those, which are significantly depleted:
sig_norm_MassSpecData <- norm_MassSpecData[norm_MassSpecData$padj.PTex_0015 <= 0.01 & norm_MassSpecData$padj.PTex_015 <= 0.01 & norm_MassSpecData$padj.PTex_15 <= 0.01,]
dim(sig_norm_MassSpecData)
[1] 3042 302
sig_norm_MassSpecData <- sig_norm_MassSpecData[sig_norm_MassSpecData$FC.PTex_0015.mean > 0 & sig_norm_MassSpecData$FC.PTex_015.mean > 0 & sig_norm_MassSpecData$FC.PTex_15.mean > 0,]
dim(sig_norm_MassSpecData)
[1] 3037 302
FC <- colnames(norm_MassSpecData)[251:268]
## Input 0.015
padj_co <- norm_MassSpecData$padj.Input_0015 <= 0.01
padj_co[which(padj_co)] <- "significant"
padj_co[which(padj_co==FALSE)] <- "non-significant"
fc_input_0015_scatter <- ggpairs(cbind(norm_MassSpecData[,FC[1:3]], padj_co),
columns = 1:3,
mapping = ggplot2::aes(colour = padj_co, alpha = 0.5),
lower = list(continuous = wrap("cor", size = 5)),
upper = list(continuous = "smooth"),
diag = list(continuous = "densityDiag")) + scatter_theme
## Input 0.15
padj_co <- norm_MassSpecData$padj.Input_015 <= 0.01
padj_co[which(padj_co)] <- "significant"
padj_co[which(padj_co==FALSE)] <- "non-significant"
fc_input_015_scatter <- ggpairs(cbind(norm_MassSpecData[,FC[4:6]], padj_co),
columns = 1:3,
mapping = ggplot2::aes(colour = padj_co, alpha = 0.5),
lower = list(continuous = wrap("cor", size = 5)),
upper = list(continuous = "smooth"),
diag = list(continuous = "densityDiag")) + scatter_theme
## Input 1.5
padj_co <- norm_MassSpecData$padj.Input_15 <= 0.01
padj_co[which(padj_co)] <- "significant"
padj_co[which(padj_co==FALSE)] <- "non-significant"
fc_input_15_scatter <- ggpairs(cbind(norm_MassSpecData[,FC[7:9]], padj_co),
columns = 1:3,
mapping = ggplot2::aes(colour = padj_co, alpha = 0.5),
lower = list(continuous = wrap("cor", size = 5)),
upper = list(continuous = "smooth"),
diag = list(continuous = "densityDiag")) + scatter_theme
## PTex 0.015
padj_co <- norm_MassSpecData$padj.PTex_0015 <= 0.01
padj_co[which(padj_co)] <- "significant"
padj_co[which(padj_co==FALSE)] <- "non-significant"
fc_ptex_0015_scatter <- ggpairs(cbind(norm_MassSpecData[,FC[10:12]], padj_co),
columns = 1:3,
mapping = ggplot2::aes(colour = padj_co, alpha = 0.5),
lower = list(continuous = wrap("cor", size = 5)),
upper = list(continuous = "smooth"),
diag = list(continuous = "densityDiag")) + scatter_theme
## PTex 0.15
padj_co <- norm_MassSpecData$padj.PTex_015 <= 0.01
padj_co[which(padj_co)] <- "significant"
padj_co[which(padj_co==FALSE)] <- "non-significant"
fc_ptex_015_scatter <- ggpairs(cbind(norm_MassSpecData[,FC[13:15]], padj_co),
columns = 1:3,
mapping = ggplot2::aes(colour = padj_co, alpha = 0.5),
lower = list(continuous = wrap("cor", size = 5)),
upper = list(continuous = "smooth"),
diag = list(continuous = "densityDiag")) + scatter_theme
## PTex 1.5
padj_co <- norm_MassSpecData$padj.PTex_15 <= 0.01
padj_co[which(padj_co)] <- "significant"
padj_co[which(padj_co==FALSE)] <- "non-significant"
fc_ptex_15_scatter <- ggpairs(cbind(norm_MassSpecData[,FC[16:18]], padj_co),
columns = 1:3,
mapping = ggplot2::aes(colour = padj_co, alpha = 0.5),
lower = list(continuous = wrap("cor", size = 5)),
upper = list(continuous = "smooth"),
diag = list(continuous = "densityDiag")) + scatter_theme
fc_input_0015_scatter
fc_input_015_scatter
fc_input_15_scatter
fc_ptex_0015_scatter
fc_ptex_015_scatter
fc_ptex_15_scatter
## Input 0.015
padj_co <- norm_MassSpecData$padj.Input_0015 <= 0.01
padj_co[which(padj_co)] <- "significant"
padj_co[which(padj_co==FALSE)] <- "non-significant"
fc_input_0015_volcano <- ggplot(data=cbind(norm_MassSpecData, padj_co), aes(x=FC.Input_0015.mean, y=-log10(padj.Input_0015), colour = padj_co ) ) +
geom_point(alpha=0.5, size=1.75) +
# xlim(c(-6, 6)) + ylim(c(0, 10)) +
xlab("log2 fold change") + ylab("-log10 adj. p-value")
## Input 0.15
padj_co <- norm_MassSpecData$padj.Input_015 <= 0.01
padj_co[which(padj_co)] <- "significant"
padj_co[which(padj_co==FALSE)] <- "non-significant"
fc_input_015_volcano <- ggplot(data=cbind(norm_MassSpecData, padj_co), aes(x=FC.Input_015.mean, y=-log10(padj.Input_015), colour = padj_co ) ) +
geom_point(alpha=0.5, size=1.75) +
# xlim(c(-6, 6)) + ylim(c(0, 10)) +
xlab("log2 fold change") + ylab("-log10 adj. p-value")
## Input 1.5
padj_co <- norm_MassSpecData$padj.Input_15 <= 0.01
padj_co[which(padj_co)] <- "significant"
padj_co[which(padj_co==FALSE)] <- "non-significant"
fc_input_15_volcano <- ggplot(data=cbind(norm_MassSpecData, padj_co), aes(x=FC.Input_15.mean, y=-log10(padj.Input_15), colour = padj_co ) ) +
geom_point(alpha=0.5, size=1.75) +
# xlim(c(-6, 6)) + ylim(c(0, 10)) +
xlab("log2 fold change") + ylab("-log10 adj. p-value")
## PTex 0.015
padj_co <- norm_MassSpecData$padj.PTex_0015 <= 0.01
padj_co[which(padj_co)] <- "significant"
padj_co[which(padj_co==FALSE)] <- "non-significant"
fc_ptex_0015_volcano <- ggplot(data=cbind(norm_MassSpecData, padj_co), aes(x=FC.PTex_0015.mean, y=-log10(padj.PTex_0015), colour = padj_co ) ) +
geom_point(alpha=0.5, size=1.75) +
# xlim(c(-6, 6)) + ylim(c(0, 10)) +
xlab("log2 fold change") + ylab("-log10 adj. p-value")
## PTex 0.15
padj_co <- norm_MassSpecData$padj.PTex_015 <= 0.01
padj_co[which(padj_co)] <- "significant"
padj_co[which(padj_co==FALSE)] <- "non-significant"
fc_ptex_015_volcano <- ggplot(data=cbind(norm_MassSpecData, padj_co), aes(x=FC.PTex_015.mean, y=-log10(padj.PTex_015), colour = padj_co ) ) +
geom_point(alpha=0.5, size=1.75) +
# xlim(c(-6, 6)) + ylim(c(0, 10)) +
xlab("log2 fold change") + ylab("-log10 adj. p-value")
## PTex 1.5
padj_co <- norm_MassSpecData$padj.PTex_15 <= 0.01
padj_co[which(padj_co)] <- "significant"
padj_co[which(padj_co==FALSE)] <- "non-significant"
fc_ptex_15_volcano <- ggplot(data=cbind(norm_MassSpecData, padj_co), aes(x=FC.PTex_15.mean, y=-log10(padj.PTex_15), colour = padj_co ) ) +
geom_point(alpha=0.5, size=1.75) +
# xlim(c(-6, 6)) + ylim(c(0, 10)) +
xlab("log2 fold change") + ylab("-log10 adj. p-value")
fc_input_0015_volcano
fc_input_015_volcano
fc_input_15_volcano
fc_ptex_0015_volcano
fc_ptex_015_volcano
fc_ptex_15_volcano
Tidy up:
rm(list = ls(pattern = "_scatter"))
rm(list = ls(pattern = "_volcano"))
rm(padj_co)
To assess performance of PTex to find RBPs, the significantly enriched proteins are compared to other studies. The following studies are taken into account: - Gerstberger review 2014 - Landthaler HEK293 interactome capture - Preiss - SONAR (annotated and predicted) - Hubstenberger P-Body proteins - RICK (high, low and unique) - CARIC
## Gerstberger review (2014) RBPs
ge <- read.csv("inputdata/RBP table-Table 1.csv")
## Gerstberger review (2014) TFs
tf <- read.csv("inputdata/human TFs-Table 1.csv")
## Human mRNA interactome capture data:
ic <- read.csv("inputdata/2015-06-09_human_interactomes.csv",na.strings=c("", "NA") )
## Preiss
preiss_gn <- read.csv("inputdata/preiss_genenames.csv", header=T, sep="\t")
## annotated RBPs from SONAR paper (Brannan et al.)
sonar_all <- read.csv("inputdata/Brannan_annotated.txt", header = FALSE)
## Predicted SONAR proteins (with score > 0.79, see Brannan et al. Mol Cell 2016)
sonar_079 <- read.csv("inputdata/Brannan_SONAR_0.79.txt", header = FALSE)
## Hubstenberger P-Body Proteins
hubst <- read.csv("inputdata/hubstenberger.csv", header = TRUE, sep = "\t")
## RICK
rick_high <- read.csv("inputdata/RICK_high_conf.csv", sep = "\t", stringsAsFactors = F)
rick_low <- read.csv("inputdata/RICK_low_conf.csv", sep = "\t", stringsAsFactors = F)
rick_unique <- read.csv("inputdata/RICK_unique.csv", sep="\t", stringsAsFactors = F)
## CARIC
caric <- read.csv("inputdata/caric.csv", sep = "\t", stringsAsFactors = F)
A matching table is created to perform the matching and store the results. It contains the following identifier columns: - Majority.protein.IDs: the Majority.protein.IDs of the significantly enriched PTex hits - MPIDsNoIso: Majority.protein.IDs with isoforms resolved to canonical form - gene_name: the gene names of the significantly enriched PTex hits
matching_table <- data.frame(Majority.protein.IDs = as.character(sig_norm_MassSpecData$Majority.protein.IDs))
matching_table$Majority.protein.IDs <- apply(X = matching_table, MARGIN = 1, FUN = function(x)unlist(strsplit(as.character(x), split=";")))
matching_table$MPIDsNoIso <- lapply(strsplit(gsub("-[0-9]{1,2}","",sig_norm_MassSpecData$Majority.protein.IDs),split=";"), function(x)unique(x))
matching_table$gene_name <- sig_norm_MassSpecData$Gene.names
The canonical MPIDs were matched with all reviewed human UniProt (SwissProt) entries.
all_rev_uniprot <- read.table("inputdata/human_proteome_reviewed_291118.list", header=F, col.names = "uniprot")
MPIDsNoIso_rev_stat <- apply(matching_table, 1, function(x) unlist(x$MPIDsNoIso) %in% all_rev_uniprot$uniprot)
MPIDsNoIso.rev <- mapply(x=matching_table$MPIDsNoIso, y=MPIDsNoIso_rev_stat, function(x,y)unlist(x[unlist(y)]))
MPIDsNoIso.rev[unlist(lapply(MPIDsNoIso.rev, function(x)length(x)==0))] <- NA
sum(is.na(MPIDsNoIso.rev))
[1] 16
matching_table$MPIDr <- MPIDsNoIso.rev
For 16 majority protein ID groups no SwissProt entry could be found.
datatable(matching_table[which(MPIDsNoIso.rev%in%"NA"),])
Those 16 hits were subjected to manual curation, meaning the accession numbers and gene names were used for a UniProt query. If an unambiguous hit was found it was corrected. The following were corrected:
matching_table$MPIDr[74] <- "P43243"
matching_table$MPIDr[83] <- "O75122"
matching_table$MPIDr[93] <- "Q9UBX3"
matching_table$MPIDr[134] <- "O95819"
matching_table$MPIDr[226] <- "Q9UPN3"
matching_table$MPIDr[264] <- "Q96MU7"
matching_table$MPIDr[268] <- "P36776"
matching_table$MPIDr[674] <- "P0DMV8"
matching_table$MPIDr[2937] <- "P0DPB6"
matching_table$MPIDr[3034] <- "P17980"
matching_table$MPIDr[3035] <- "Q9UKV3"
After manual correction, the following were still not identifiable.
datatable(matching_table[which(matching_table$MPIDr%in%"NA"),])
These hits were excluded from further analyses.
matching_table <- matching_table[-c(162,169,178,896,3037),]
datatable(matching_table[which(matching_table$MPIDr%in%"NA"),])
WARNING:235 Q13404;A5PLL7 UBE2V1;TMEM189 T;F
stays! Others might, too!
## Gerstberger RBPs
matching_table$Gerstberger.RBP <- apply(matching_table,1,function(x) any(ge$gene.name %in% unlist(strsplit(as.character(x$gene_name),split=";"))))
## Gerstberger TFs (negative control)
matching_table$Gerstberger.TF <- apply(matching_table,1,function(x) any(tf$gene.name %in% unlist(strsplit(as.character(x$gene_name),split=";"))))
## Landthaler HEK293 interactome capture data
hekmRBP <- subset(ic, ic$HEK293 == "mRNA interactome")
matching_table$Landthaler.mRBP <- apply(matching_table, 1, function(x) any(hekmRBP$Uniprot.entry %in% unlist(x$MPIDr)))
## Preiss
matching_table$Preiss <- apply(matching_table, 1, function(x) any(preiss_gn$gene.name %in% unlist(strsplit(as.character(x$gene_name),split=";"))))
## Annotated RBPs (from the SONAR paper)
matching_table$Brannan.annotated <- apply(matching_table, 1, function(x) any(sonar_all$V1 %in% unlist(strsplit(as.character(x$gene_name),split=";"))))
## SONAR-predicted RBPs
matching_table$Brannan.predicted <- apply(matching_table, 1, function(x) any(sonar_079$V1 %in% unlist(strsplit(as.character(x$gene_name),split=";"))))
## Hubstenberger P-Body proteins
matching_table$Hubstenberger.PBP <- apply(matching_table, 1, function(x) any(hubst$gene.name %in% unlist(strsplit(as.character(x$gene_name),split=";"))))
## RICK data
matching_table$Rick.high <- apply(matching_table, 1, function(x) any(rick_high$Protein_ID %in% unlist(x$MPIDr)))
matching_table$Rick.low <- apply(matching_table, 1, function(x) any(rick_low$Protein_ID %in% unlist(x$MPIDr)))
matching_table$Rick.unique <- apply(matching_table, 1, function(x) any(rick_unique$Protein_ID %in% unlist(x$MPIDr)))
## CARIC RBPs
matching_table$Caric <- apply(matching_table, 1, function(x) any(caric$UniProt.accession %in% unlist(x$MPIDr)))
Note that matching via stringsplitted gene names can produce multiple hits in reference for a single PTex hit.
# inPTex, not inPTex
matching_df <- data.frame(
match = c("yes", "no"),
Gerstberger.RBPs = c(round(sum(matching_table$Gerstberger.RBP)/nrow(ge),4), round((nrow(ge) - sum(matching_table$Gerstberger.RBP))/nrow(ge),4)),
Gerstberger.TFs =c(round(sum(matching_table$Gerstberger.TF)/nrow(tf),4), round((nrow(tf) - sum(matching_table$Gerstberger.TF))/nrow(tf),4)),
Landthaler = c(round(sum(matching_table$Landthaler.mRBP)/nrow(hekmRBP),4), round((nrow(hekmRBP) - sum(matching_table$Landthaler.mRBP))/nrow(hekmRBP),4)),
Preiss = c(round(sum(matching_table$Preiss)/nrow(preiss_gn),4), round((nrow(preiss_gn)-sum(matching_table$Preiss))/nrow(preiss_gn),4)),
Brannan.annotated = c(round(sum(matching_table$Brannan.annotated)/nrow(sonar_all),4), round((nrow(sonar_all) - sum(matching_table$Brannan.annotated))/nrow(sonar_all),4)),
Brannan.predicted = c(round(sum(matching_table$Brannan.predicted)/nrow(sonar_079),4), round((nrow(sonar_079) - sum(matching_table$Brannan.predicted))/nrow(sonar_079),4)),
Hubstenberger.PBP = c(round(sum(matching_table$Hubstenberger.PBP)/nrow(hubst),4), round((nrow(hubst) - sum(matching_table$Hubstenberger.PBP))/nrow(hubst),4)),
Rick.high = c(round(sum(matching_table$Rick.high)/nrow(rick_high),4), round((nrow(rick_high) - sum(matching_table$Rick.high))/nrow(rick_high),4)),
Rick.low = c(round(sum(matching_table$Rick.low)/nrow(rick_low),4), round((nrow(rick_low) - sum(matching_table$Rick.low))/nrow(rick_low),4)),
Rick.unique = c(round(sum(matching_table$Rick.unique)/nrow(rick_unique),4), round((nrow(rick_unique) - sum(matching_table$Rick.unique))/nrow(rick_unique),4)),
Caric = c(round(sum(matching_table$Caric)/nrow(caric),4), round((nrow(caric) - sum(matching_table$Caric))/nrow(caric),4))
)
ggplot(melt(matching_df, id.vars = "match"), aes(x=variable, y=value, fill=match)) +
geom_bar(stat = "identity", alpha=.6) +
ylab("fraction") + xlab("") +
theme(axis.text.x = element_text(angle = 45, hjust = 1))
The significantly enriched hits are annotated with - isoelectric point - molecular weight - hydrophobicity - (RBD) - (GO)
For that a list of UniProt accession numbers is needed. For that the MPIDr
of the matching table is used, while for entries with multiple accession numbers, only the first is used.
accessions <- unlist(lapply(X=matching_table$MPIDr, FUN = function(x) strsplit(as.character(x), split = ";")[[1]][1]))
write.table(accessions, "accessions.tsv", row.names = F, col.names = F)
For comparison of the MS data with the human proteome a dataset from isoelectricpointdb.org
was retrieved (including isoelectric points, molecular weights and sequences) (as of 29.11.18):
isoelectricpointdb <- read.csv("inputdata/UP000005640_9606_all.fasta.pI.csv", header=TRUE, sep=",")
IPDB_matching <- data.frame(
UniProt = accessions,
Sequence = rep(NA,length(accessions)),
MolWeight = rep(NA,length(accessions)),
IPC_protein = rep(NA,length(accessions)),
Hydrophobicity = rep(NA,length(accessions))
)
for(i in seq(nrow(IPDB_matching))){
try(IPDB_matching$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|",IPDB_matching$UniProt[i],"|", sep=""), x = isoelectricpointdb$header, fixed = TRUE)]))
try(IPDB_matching$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|",IPDB_matching$UniProt[i],"|", sep=""), x = isoelectricpointdb$header, fixed = TRUE)])
try(IPDB_matching$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|",IPDB_matching$UniProt[i],"|", sep=""), x = isoelectricpointdb$header, fixed = TRUE)])
}
Error in IPDB_matching$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Not found: P0DPB6 which is >sp|Q9Y2S0|RPAC2_HUMAN DNA-directed RNA polymerases I and III subunit RPAC2 OS=Homo sapiens GN=POLR1D PE=1 SV=1
for(i in seq(nrow(IPDB_matching))){
try(IPDB_matching$Hydrophobicity[i] <- aaComp(IPDB_matching$Sequence[i])[[1]]["NonPolar","Mole%"])
}
Sequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculated
all_rev_uniprot
were matched with the isoelectricpointdb. (Note that the following chunk runs very long, because of the low speed of for loops)
IPDB_matching_proteome <- data.frame(
UniProt = as.character(all_rev_uniprot$uniprot),
Sequence = rep(NA,length(all_rev_uniprot)),
MolWeight = rep(NA,length(all_rev_uniprot)),
IPC_protein = rep(NA,length(all_rev_uniprot)),
Hydrophobicity = rep(NA,length(all_rev_uniprot))
)
for(i in seq(nrow(IPDB_matching_proteome))){
try(IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|",IPDB_matching_proteome$UniProt[i],"|", sep=""), x = isoelectricpointdb$header, fixed = TRUE)]))
try(IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|",IPDB_matching_proteome$UniProt[i],"|", sep=""), x = isoelectricpointdb$header, fixed = TRUE)])
try(IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|",IPDB_matching_proteome$UniProt[i],"|", sep=""), x = isoelectricpointdb$header, fixed = TRUE)])
}
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$Sequence[i] <- as.character(isoelectricpointdb$sequence[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$MolWeight[i] <- isoelectricpointdb$molecular_weight[grep(pattern = paste("|", :
replacement has length zero
Error in IPDB_matching_proteome$IPC_protein[i] <- isoelectricpointdb$IPC_protein[grep(pattern = paste("|", :
replacement has length zero
for(i in seq(nrow(IPDB_matching_proteome))){
try(IPDB_matching_proteome$Hydrophobicity[i] <- aaComp(IPDB_matching_proteome$Sequence[i])[[1]]["NonPolar","Mole%"])
}
Sequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculatedSequence 1 has unrecognized amino acid types. Output value might be wrong calculated
Some of the accession numbers were not included in the isoelectricpointdb.
sum(sapply(IPDB_matching_proteome$Sequence, function(x)is.na(x)))
[1] 173
sum(sapply(IPDB_matching_proteome$MolWeight, function(x)is.na(x)))
[1] 173
sum(sapply(IPDB_matching_proteome$IPC_protein, function(x)is.na(x)))
[1] 173
sum(sapply(IPDB_matching_proteome$Hydrophobicity, function(x)is.nan(x)))
[1] 173
mw_distribution <- data.frame(
MolWeight = c(IPDB_matching$MolWeight, IPDB_matching_proteome$MolWeight),
set = c(rep("PTex", length(IPDB_matching$MolWeight)), rep("Proteome", length(IPDB_matching_proteome$MolWeight)))
)
ggplot(mw_distribution, aes(x = set, y = MolWeight)) +
geom_boxplot() +
scale_y_log10() +
xlab("") +
ylab("Molecular Weight")
pdf("MolWeight_boxplot.pdf", width = 10, height = 7)
last_plot()
dev.off()
png
2
pi_distribution <- data.frame(
IPC_protein = c(IPDB_matching$IPC_protein, IPDB_matching_proteome$IPC_protein),
set = c(rep("PTex", length(IPDB_matching$IPC_protein)), rep("Proteome", length(IPDB_matching_proteome$IPC_protein)))
)
ggplot(pi_distribution, aes(x = set, y = IPC_protein)) +
geom_boxplot() +
xlab("") +
ylab("IPC_protein")
pdf("IPC_protein_boxplot.pdf", width = 10, height = 7)
last_plot()
dev.off()
png
2
A density plot of the IPC_protein distributions comparing PTex, Landthaler, Rick unique, Rick high and proteome is prepared.
rick_high_ip <- data.frame(
IPC_protein = IPDB_matching_proteome$IPC_protein[IPDB_matching_proteome$UniProt %in% rick_high$Protein_ID],
set = rep("Rick.high", nrow(rick_high))
)
rick_unique_ip <- data.frame(
IPC_protein = IPDB_matching_proteome$IPC_protein[IPDB_matching_proteome$UniProt %in% rick_unique$Protein_ID],
set = rep("Rick.unique", nrow(rick_unique))
)
# 6 accessions of the Landthaler data are not included in the isoelectricpointdb and will be removed
landthaler_ip <- data.frame(
IPC_protein = IPDB_matching_proteome$IPC_protein[IPDB_matching_proteome$UniProt %in% hekmRBP$Uniprot.entry[-which(hekmRBP$Uniprot.entry %in% IPDB_matching_proteome$UniProt==FALSE)]],
set = rep("Landthaler.mRBP", length(which(hekmRBP$Uniprot.entry %in% IPDB_matching_proteome$UniProt==TRUE)))
)
ip_density_distribution <- data.frame(
IPC_protein = c(IPDB_matching$IPC_protein, landthaler_ip$IPC_protein, rick_unique_ip$IPC_protein, rick_high_ip$IPC_protein, IPDB_matching_proteome$IPC_protein),
set = c(rep("PTex", nrow(IPDB_matching)), as.character(landthaler_ip$set), as.character(rick_unique_ip$set), as.character(rick_high_ip$set), rep("Proteome", nrow(IPDB_matching_proteome)))
)
ggplot2::ggplot(ip_density_distribution, aes(x = IPC_protein, colour = set)) +
geom_density()
pdf("IPC_protein_density.pdf", width = 10, height = 7)
last_plot()
dev.off()
png
2
hydrophobicity_distribution <- data.frame(
Hydrophobicity = c(IPDB_matching$Hydrophobicity, IPDB_matching_proteome$Hydrophobicity),
set = c(rep("PTex", length(IPDB_matching$Hydrophobicity)), rep("Proteome", length(IPDB_matching_proteome$Hydrophobicity)))
)
ggplot(hydrophobicity_distribution, aes(x = set, y = Hydrophobicity)) +
geom_boxplot() +
xlab("") +
ylab("Hydrophobicity")
pdf("Hydrophobicity_boxplot.pdf", width = 10, height = 7)
last_plot()
dev.off()
png
2
The RBD domain annotation is performed using DAVID online tool. Since it only accepts lists with maximum 3000 entries 10 randomly sampled lists were created.
set.seed(42)
accessions_S1 <- sample(accessions, 3000)
accessions_S2 <- sample(accessions, 3000)
accessions_S3 <- sample(accessions, 3000)
accessions_S4 <- sample(accessions, 3000)
accessions_S5 <- sample(accessions, 3000)
accessions_S6 <- sample(accessions, 3000)
accessions_S7 <- sample(accessions, 3000)
accessions_S8 <- sample(accessions, 3000)
accessions_S9 <- sample(accessions, 3000)
accessions_S10 <- sample(accessions, 3000)
write.table(accessions_S1, "accessions_S1.tsv", row.names = F, col.names = F)
write.table(accessions_S2, "accessions_S2.tsv", row.names = F, col.names = F)
write.table(accessions_S3, "accessions_S3.tsv", row.names = F, col.names = F)
write.table(accessions_S4, "accessions_S4.tsv", row.names = F, col.names = F)
write.table(accessions_S5, "accessions_S5.tsv", row.names = F, col.names = F)
write.table(accessions_S6, "accessions_S6.tsv", row.names = F, col.names = F)
write.table(accessions_S7, "accessions_S7.tsv", row.names = F, col.names = F)
write.table(accessions_S8, "accessions_S8.tsv", row.names = F, col.names = F)
write.table(accessions_S9, "accessions_S9.tsv", row.names = F, col.names = F)
write.table(accessions_S10, "accessions_S10.tsv", row.names = F, col.names = F)
GO term analyses was performed by the PANTHER online tool using the accessions
table.
A master table containing identifiers, enrichments, matches and annotations is created.
# create vector holding rows of sig_norm_MassSpecData that are in matching_table
MSD_to_MT <- which(sapply(X = sig_norm_MassSpecData$Majority.protein.IDs, FUN = function(x)unlist(strsplit(as.character(x), split=";"))) %in% matching_table$Majority.protein.IDs)
master_table <- data.frame(
UniProt = accessions,
Majority.protein.IDs = sig_norm_MassSpecData$Majority.protein.IDs[MSD_to_MT],
MPID.reviewed = as.character(matching_table$MPIDr),
Protein.name = sig_norm_MassSpecData$Protein.names[MSD_to_MT],
Gene.name = matching_table$gene_name,
FC.PTex_0015.mean = sig_norm_MassSpecData$FC.PTex_0015.mean[MSD_to_MT],
padj.PTex_0015 = sig_norm_MassSpecData$padj.PTex_0015[MSD_to_MT],
FC.PTex_015.mean = sig_norm_MassSpecData$FC.PTex_015.mean[MSD_to_MT],
padj.PTex_015 = sig_norm_MassSpecData$padj.PTex_015[MSD_to_MT],
FC.PTex_15.mean = sig_norm_MassSpecData$FC.PTex_15.mean[MSD_to_MT],
padj.PTex_15 = sig_norm_MassSpecData$padj.PTex_15[MSD_to_MT],
Gerstberger.RBP = matching_table$Gerstberger.RBP,
Gerstberger.TF = matching_table$Gerstberger.TF,
Landthaler.mRBP = matching_table$Landthaler.mRBP,
Preiss = matching_table$Preiss,
Brannan.annotated = matching_table$Brannan.annotated,
Brannan.predicted = matching_table$Brannan.predicted,
Hubstenberger.PBP = matching_table$Hubstenberger.PBP,
Rick.high = matching_table$Rick.high,
Rick.low = matching_table$Rick.low,
Rick.unique = matching_table$Rick.unique,
Caric = matching_table$Caric,
IPC_protein = IPDB_matching$IPC_protein,
MolWeight = IPDB_matching$MolWeight,
Hydrophobicity = IPDB_matching$Hydrophobicity
)
write.table(master_table, "master_table.tsv", sep = "\t", row.names = F)
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux
Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblas_haswellp-r0.3.3.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DT_0.4 Peptides_2.4 GGally_1.4.0 ggplot2_3.0.0 reshape2_1.4.3 limma_3.36.3 dplyr_0.7.6
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 later_0.7.4 RColorBrewer_1.1-2 pillar_1.3.0 compiler_3.5.1 plyr_1.8.4 bindr_0.1.1 base64enc_0.1-3
[9] tools_3.5.1 digest_0.6.17 jsonlite_1.5 evaluate_0.11 tibble_1.4.2 gtable_0.2.0 pkgconfig_2.0.2 rlang_0.2.2
[17] shiny_1.1.0 rstudioapi_0.7 crosstalk_1.0.0 yaml_2.2.0 bindrcpp_0.2.2 withr_2.1.2 stringr_1.3.1 knitr_1.20
[25] htmlwidgets_1.2 rprojroot_1.3-2 grid_3.5.1 tidyselect_0.2.4 reshape_0.8.7 glue_1.3.0 R6_2.3.0 rmarkdown_1.10
[33] purrr_0.2.5 magrittr_1.5 promises_1.0.1 backports_1.1.2 scales_1.0.0 htmltools_0.3.6 assertthat_0.2.0 xtable_1.8-3
[41] mime_0.5 colorspace_1.3-2 httpuv_1.4.5 labeling_0.3 stringi_1.2.4 lazyeval_0.2.1 munsell_0.5.0 crayon_1.3.4