dot-checkSetupGroups: Additional/final Check And Adjustments To Sample-order After...

In wrProteo: Proteomics Data Analysis Functions

Additional/final Check And Adjustments To Sample-order After readSampleMetaData()

Description

This (low-level) function performs an additional/final check & adjustments to sample-names after readSampleMetaData()

Usage

.checkSetupGroups(
  abund,
  setupSd,
  gr = NULL,
  sampleNames = NULL,
  quantMeth = NULL,
  silent = FALSE,
  callFrom = NULL,
  debug = FALSE
)

Arguments

abund	(matrix or data.frame) abundance data, only the colnames will be used
setupSd	(list) describing sammple-setup, typically produced by readSampleMetaData() (from this package)
gr	(factor) optional custom information about replicate-layout, has priority over setupSd
sampleNames	(character) custom sample-names, has priority over abund and setuoSd
quantMeth	(character) 2-letter abbreviation of name of quantitation-software (eg 'MQ')
silent	(logical) suppress messages
callFrom	(character) allow easier tracking of messages produced
debug	(logical) display additional messages for debugging

Details

In particular, when no meta-data or expriental setup was found this function tries to get a min of information

Value

This function returns an enlaged/updated list 'setupSd' (set setupSd$sampleNames, setupSd$groups)

See Also

used in readProtDiscovererFile, readMaxQuantFile, readProlineFile, readFragpipeFile

Examples

abun1 <- matrix(1:16, ncol=8, dimnames=list(NULL,paste("samp", LETTERS[8:1], sep="_")))
sdrf1 <- data.frame(source.name=paste(rep(LETTERS[1:4],each=2), 1:2, sep="_"), 
  assay.name=paste0("run", 1:8), comment.data.file.=paste0("MSrun", 8:1))
setU1 <- list(level=gl(4,2), meth="lowest", sampleNames=paste("samp", LETTERS[1:8], sep="_"), 
  sdrfDat=sdrf1, annotBySoft=NULL)
.checkSetupGroups(abun1, setU1)

wrProteo documentation built on July 24, 2026, 1:06 a.m.