#
# 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 groups file
packagePath <- path.package("SRMService")
packagePath <- "."
proteinGroupsFile <-
file.path(packagePath,
"/inst/samples/genericQuantMatrix",
"Generic_QuantMatrix.txt")
# read in protein groups file
protein <- readr::read_tsv(proteinGroupsFile)
colnames(protein) <- make.names(colnames(protein))
# important structure for protein matrix
#colnames(protein)
# "Majority.protein.IDs" "Intensity.dnmt3b_15_s1" "Intensity.dnmt3b_15_s2" "Intensity.dnmt3l_11_s1" "Intensity.dnmt3l_11_s2" "Intensity.IP_lsh_s1" "Intensity.IP_lsh_s2" "Intensity.WT" "Peptides" "Fasta.headers"
# fix column names in order to parse all efficientl
# also add some columns that are not by default present
# "Majority.protein.IDs"
# Peptides
# Fasta.headers
originalHeaders <- colnames(protein)
fakeNrPeptides <- rep(3, nrow(protein))
fakeFastaHeader <- rep("No_Description", nrow(protein))
protein <- cbind(protein, fakeNrPeptides, fakeFastaHeader)
# for project p2482 put the sample annotations from metainfo
newHeaders <-
c(
"Majority.protein.IDs",
paste("Intensity.", originalHeaders[2:length(originalHeaders)], sep = ""),
"Peptides",
"Fasta.headers"
)
colnames(protein) <- newHeaders
# all raw files in protein groups (select here for proper 2grp)
rawF <-
gsub("Intensity\\.", "", grep("Intensity\\.", colnames(protein), value =
T))
# how to parse condition from the filenames (separator in fn _ )
condition <- quantable::split2table(rawF)[, 3]
#
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
)
###################################
### Configuration section
tmpdir <- tempdir()
resultdir <- file.path(tmpdir, "GenericTwoGroup")
dir.create(resultdir)
# calls up data editor
#fix(annotation)
# default settings
Experimentname = "pXXX_compareDifferentTissues"
nrNas = sum(!is.na(annotation$Condition)) - 3
nrPeptides = 2
reference = unique(annotation$Condition)[1]
qvalueThreshold = 0.01
qfoldchange = 1
write.table(annotation, file = file.path(resultdir, "annotationused.txt"))
####### END of user configuration ##
# important structure for protein matrix
# Do the analysis
grp2 <- Grp2Analysis(
annotation,
Experimentname,
maxNA = nrNas,
nrPeptides = nrPeptides,
reference = reference,
numberOfProteinClusters = 20
)
grp2$setMQProteinGroups(protein)
grp2$setQValueThresholds(qvalue = qvalueThreshold, qfoldchange = qfoldchange)
#write out results and render pdf
#readr::write_tsv(x = grp2$getResultTable(), path = file.path(resultdir,"pValues.csv"))
genericQuantMatrixGRP2 <- grp2
usethis::use_data(genericQuantMatrixGRP2, overwrite = TRUE)
## REMOVE TO RENDER
#rmarkdown::render("vignettes/Grp2Analysis.Rmd", params = list(grp = genericQuantMatrixGRP2), envir = new.env())
# rmarkdown::render("vignettes/Grp2AnalysisHeatmap3.Rmd",bookdown::pdf_document2(), params=list(grp = grp2))
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