inst/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R

In protViz/SRMService: Report Quantitative Mass Spectrometry Data

#
# 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
packagedir <- path.package("SRMService")

####! set the path to the proteinGroups.txt file.
proteinGroupsFile <-
  file.path(packagedir, "samples/proteinGroups/proteinGroups.txt")

###


protein <- readr::read_tsv(proteinGroupsFile)
colnames(protein) <- make.names(colnames(protein))
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')

##
rawF <-
  gsub("Intensity\\.", "", grep("Intensity\\.", colnames(protein), value =
                                  T))

condition <- quantable::split2table(rawF)[, 3]

# Raw.file <- c("23bb","23bcd","23ddd","","","")
# condition <- c("baseline","baseline","w1","w1")

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
resultdir <- "output"
dir.create(resultdir)

#fix(annotation)

Experimentname = ""
nrNas = sum(!is.na(annotation$Condition)) - 1
nrNas = 5
nrPeptides = 2
reference = unique(annotation$Condition)[1]
reference = "WT"
qvalueThreshold = 0.05
qfoldchange = 1
write.table(annotation, file = file.path(resultdir, "annotationused.txt"))

####### END of user configuration ##

# source("R/Grp2Analysis.R")
grp2 <- Grp2Analysis(
  annotation,
  "Experimentname",
  maxNA = nrNas,
  nrPeptides = nrPeptides,
  reference = reference,
  numberOfProteinClusters = 20
)

grp2$getDesignMatrix()

grp2$setMQProteinGroups(protein)
grp2$setQValueThresholds(qvalue = qvalueThreshold, qfoldchange = qfoldchange)
mqQuantMatrixGRP2 <- grp2

head(mqQuantMatrixGRP2$getModPValuesCI())

usethis::use_data(mqQuantMatrixGRP2, overwrite = TRUE)
#readr::write_tsv(grp2$getResultTable(), path=file.path(resultdir,"pValues.csv"))

## REMOVE TO RENDER
# rmarkdown::render("vignettes/Grp2AnalysisHeatmap3.Rmd",bookdown::pdf_document2(), params=list(grp = grp2))
# rmarkdown::render("vignettes/Grp2Analysis.Rmd",bookdown::pdf_document2(), params=list(grp = grp2))