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 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)

wrProteo documentation built on April 12, 2025, 1:16 a.m.