updateSymbolsToValidKeys {annotate} | R Documentation

## 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)

[Package annotate version 1.20.1 Index]