.extrSpecPref: Extract Additional Information To Construct The 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). In order to compare specPref a species-column will be added to the annotation (annot) - if not already present 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
)

Value

This function returns a matrix with additional column 'SpecType'

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

Details

Different to readSampleMetaData this function also considers the main annotation as axtracted with main quantification data. For example, this function can complement protein annotation data if columns 'Accession','EntryName' or 'SpecType' are missing

Examples

Run this code

annot1 <- cbind( Leading.razor.protein=c("sp|P00925|ENO2_YEAST",
  "sp|Q3E792|RS25A_YEAST", "sp|P09938|RIR2_YEAST", "sp|P09938|RIR2_YEAST",
  "sp|Q99186|AP2M_YEAST", "sp|P00915|CAH1_HUMAN"), 
  Species= rep(c("Saccharomyces cerevisiae","Homo sapiens"), c(5,1)))
specPref1 <- list(conta="CON_|LYSC_CHICK", 
  mainSpecies="OS=Saccharomyces cerevisiae", spike="P00915")   # MQ type
.extrSpecPref(specPref1, annot1, useColumn=c("Species","Leading.razor.protein"))