wrProteo: replMissingProtNames – R documentation

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replMissingProtNames

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,
  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
`callFrom`	(character) allow easier tracking of message(s) produced

Value

list as input, but with missing elments of $annot completed (if available in other columns)

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)

wrProteo

Proteomics Data Analysis Functions

v1.4.1

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release