#
# If you are going to use results produced by the scripts please do cite the
# SRMSerivce R package by providing the following URL
# www.github.com/protViz/SRMService
# by W.E. Wolski, J. Grossmann, C. Panse
#
library(limma)
library(SRMService)
protein <-
system.file("samples/proteinGroups/proteinGroupsPullDown.txt", package = "SRMService")
protein <- readr::read_tsv(protein)
colnames(protein) <- make.names(colnames(protein))
tmp <- strsplit(protein$Majority.protein.IDs, split = " ")
tmp2 <- sapply(tmp, function(x) {
x[1]
})
protein$Majority.protein.IDs <- gsub(">", "", tmp2)
rawF <-
gsub("Intensity\\.", "", grep("Intensity\\.", colnames(protein), value =
T))
condition <- quantable::split2table(rawF)
condition <- paste(condition[, 4], condition[, 5], sep = "_")
annotation <- data.frame(
Raw.file = rawF,
Condition = condition,
BioReplicate = paste("X", 1:length(condition), sep =
""),
Run = 1:length(condition),
IsotopeLabelType = rep("L", length(condition)),
stringsAsFactors = F
)
workdir <- "output"
dir.create(workdir)
tmp <- cumsum(rev(table(protein$Peptides)))
barplot(tmp[(length(tmp) - 5):length(tmp)], ylim = c(0, length(protein$Peptides)), xlab =
'nr of proteins with at least # peptides')
###################################
### Configuration section
Experimentname = "p2550"
nrNas = 5
nrPeptides = 2
annotation$Condition[grepl("_w$", annotation$Condition)] <- NA
reference = "pegfp_wo" # unique(annotation$Condition)[3]
#write.table(annotation, file="output/annotationused.txt")
####### END of user configuration ##
grp2 <- Grp2Analysis(
annotation,
"Experimentname",
maxNA = nrNas,
nrPeptides = nrPeptides,
reference = reference,
numberOfProteinClusters = 20
)
grp2$setMQProteinGroups(protein)
grp2$qfoldchange = 2
grp2$setQValueThresholds(qvalue = 0.01)
grp2PullDownExample <- grp2
x2 <- grp2$getResultTable()
dim(x2)
x3 <- grp2$getResultTableWithPseudo()
dim(x3)
usethis::use_data(grp2PullDownExample, overwrite = TRUE)
results <- grp2$getResultTable()
#write.table(results, file=file.path(workdir,"pValues.csv"), quote=FALSE, sep = "\t", col.names=NA)
#rmarkdown::render("Grp2Analysis.Rmd", bookdown::pdf_document2())
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