updateSymbolsToValidKeys: Take a list of symbols and translate them into the best...

In Bioconductor/annotate: Annotation for microarrays

Take a list of symbols and translate them into the best possible ID for a package.

Description

Given a list of gene symbols and a package, find a valid ID for that package. If there isn't a valid ID, then return the original symbol.

Usage

updateSymbolsToValidKeys(symbols, pkg)

Arguments

symbols	A character vector containing gene symbols that you wish to try and translate into valid IDs.
pkg	The package name of the chip for which we wish to validate IDs.

Details

This is a convenience function for getting from a possibly varied list of gene symbols mapped onto something that is a nice concrete ID such as an entrez gene ID. When such an ID cannot be found, the original symbol will come back to prevent the loss of any information.

Value

This function returns a vector of IDs corresponding to the symbols that were input. If the symbols don't have a valid ID, then they come back instead.

Author(s)

Marc Carlson

See Also

isValidKey

Examples

## Not run: 
  ## one "bad" ID, one that can be mapped onto a valid ID, and a 3rd
  ## which already is a valid ID
  syms <- c("15S_rRNA_2","21S_rRNA_4","15S_rRNA")
  updateSymbolsToValidKeys(syms, "org.Sc.sgd")

  ## 3 symbols and a 4th that will NOT be valid
  syms <- c("MAPK11","P38B","FLJ45465", "altSymbol")
  updateSymbolsToValidKeys(syms, "org.Hs.eg")

## End(Not run)

Bioconductor/annotate documentation built on Nov. 2, 2024, 4:40 p.m.