.extrSpecPref {wrProteo}

Extract additional information to construct colum SpecType

Description

This (low-level) function creates the column annot[,'SpecType'] which may help distinguishing different lines/proteins. This information may, for example, be used to normalize only to all proteins of a common backgroud matrix (species). If $mainSpecies or $conta: match to annot[,"Species"], annot[,"EntryName"], annot[,"GeneName"], if length==1 grep in annot[,"Species"]

Usage

.extrSpecPref(
  specPref,
  annot,
  useColumn = c("Species", "EntryName", "GeneName", "Accession"),
  suplInp = NULL,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

specPref

(list) may contain $mainSpecies, $conta ...

annot

(matrix) main protein annotation

useColumn

(factor) columns from annot to use/mine

suplInp

(matrix) additional custom annotation

silent

(logical) suppress messages

debug

(logical) display additional messages for debugging (starting with 'mainSpecies','conta' and others - later may overwrite prev settings)

callFrom

(character) allow easier tracking of messages produced

Value

This function returns a matrix with additional column 'SpecType'

See Also

used in readProtDiscovererFile, readMaxQuantFile, readProlineFile, readFragpipeFile

Examples

.commonSpecies()