getSYMBOL {annotate}R Documentation

Functions to deal with Data Packages

Description

The functions documented here are intended to make it easier to map from a set of manufacturers identifiers (such as you will get from the chips etc) to other identifiers.

Usage

getSYMBOL(x, data)
getLL(x, data)
getGO(x, data)
getPMID(x, data)
getGOdesc(x, which=c("MF","BP","CC") )
contents(object)

Arguments

x The identifiers to be mapped (usually manufacturer)
data A character string identifying the data source
which For getGOdesc indicates which GO hierarchy to use.
object The environment (data table) that you want to get all contents from

Details

Appropriate translations are done. In some cases such as getLL and getSYMBOL there will only be one match and a vector is returned. In other cases such as getPMID and getGO there may be multiple matches and a list is returned. For getGOdesc the input vector is GO identifiers (not manufacturer identifiers) and in the output any identifier that does not have a description in the selected GO hierarchy (MF, BP or CC) is dropped.

Value

Either a vector or a list depending on whether multiple values per input are possible.

Author(s)

R. Gentleman

See Also

multiget

Examples

  data(eset)
  gN <- geneNames(eset)[100:105]
   ## A bit of a hack to not have a package dependency on hgu95av2
   ## but need to fiddle w/ the warn level to not fail the example anyways.
   curWarn <- getOption("warn")
   options(warn=0)
   on.exit(options(warn=curWarn), add=TRUE)
  if( require("hgu95av2", character.only=TRUE)
       && require("GO", character.only=TRUE) ) {
      getSYMBOL(gN,"hgu95av2" )
      gg<- getGO(gN, "hgu95av2")
      getGOdesc(gg[[2]], "MF")
      getLL(gN, "hgu95av2")
      getPMID(gN, "hgu95av2")
  } else
   cat("could not run all examples\n")

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