inst/RunScripts/Run_PD_QuantTwoGroupAnalysis.R

In protViz/SRMService: Report Quantitative Mass Spectrometry Data

library(readr)
library(dplyr)
library(quantable)
library(SRMService)

## specify file names

inputFilesFile <- "20161115_02_G3_InputFiles.txt"
proteinsFile <- "20161115_02_G3_Proteins.txt"
##


inputFiles <- read_tsv(inputFilesFile)
inputFileFix <- fix_PD_inputFiles(inputFiles)

annotation <- data.frame(
  Raw.file = inputFileFix$Raw.File,
  Condition = gsub("[0-9]", "", quantable::split2table(inputFileFix$Raw.File)[, 3]),
  BioReplicate = paste("X", 1:nrow(inputFileFix), sep =
                         ""),
  Run = 1:nrow(inputFileFix),
  IsotopeLabelType = rep("L", nrow(inputFileFix)),
  stringsAsFactors = F
)



proteins <- read_tsv(proteinsFile)
proteinsFIX <- remap_PD_ProteinTable(proteins, inputFiles)




###################################
### Configuration section
fix(annotation)
resultdir = "output"
dir.create(resultdir)


Experimentname = ""
nrNas = sum(!is.na(annotation$Condition)) - 1
nrPeptides = 2
reference = unique(annotation$Condition)[1]
qvalueThreshold = 0.01
qfoldchange = 2

write.table(annotation, file = file.path(resultdir, "annotationused.txt"))

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



library(SRMService)
grp2 <-
  Grp2Analysis(
    annotation,
    "test pd import",
    maxNA = nrNas  ,
    nrPeptides = nrPeptides,
    reference = reference
  )
grp2$setProteins(proteinsFIX)
grp2$setQValueThresholds(qvalue = qvalueThreshold, qfoldchange = qfoldchange)

results <- grp2$getResultTableWithPseudo()
write_tsv(results, path = file.path(resultdir, "pValues.tsv"))
rmarkdown::render("Grp2Analysis.Rmd", output_format = bookdown::pdf_document2())