inst/RunScripts/Run_Generic_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
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))