.checkSetupGroups {wrProteo}

Additional/final chek and adjustments to sample-order after readSampleMetaData()

Description

This (low-level) function performs an additional/final chek & 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 from package wrMisc

gr

(factor) optional custom information about replicate-layout, has priority over setuoSd

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

Value

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

See Also

used in readProtDiscovererFile, readMaxQuantFile, readProlineFile, readFragpipeFile

Examples

set.seed(2021)