replMissingProtNames {wrProteo}

Complement Missing EntryNames In Annotation

Description

This function helps replacing missing EntryNames (in $annot) after reading quantification results. To do so the comumn-names of annCol will be used : The content of 2nd element (and optional 3rd element) will be used to replace missing content in column defined by 1st element.

Usage

replMissingProtNames(
  x,
  annCol = c("EntryName", "Accession", "SpecType"),
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

x

(list) output of readMaxQuantFile, readProtDiscovFile or readProlineFile. This list must be a matrix and contain $annot with the columns designated in annCol.

annCol

(character) the column-names form x$annot) which will be used : The first column designs the column where empty fields are searched and the 2nd and (optional) 3rd will be used to fill the empty spots in the st column

silent

(logical) suppress messages

debug

(logical) display additional messages for debugging

callFrom

(character) allow easier tracking of message(s) produced

Value

This function returns a list (like as input), but with missing elments of $annot completed (if available in other columns)

See Also

readMaxQuantFile, readProtDiscovFile, readProlineFile

Examples

dat <- list(quant=matrix(sample(11:99,9,replace=TRUE), ncol=3), annot=cbind(EntryName=c(
  "YP010_YEAST","",""),Accession=c("A5Z2X5","P01966","P35900"), SpecType=c("Yeast",NA,NA)))
replMissingProtNames(dat)