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)
lookUp(x, data, what)
getUniqAnnItem()

Arguments

x The identifiers to be mapped (usually manufacturer)
data The basename of the meta-data package to be used.
what what a character string for the name of an annotation element of an annotation data package
which which a character string in the form of MF, BP, CC, or ANY to indicated the GO category of interests

Details

Users must supply the basename of the meta-data package that they want to use to provide the mappings. The name of the meta-data package is the same as the basename.

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.

lookUp is a general function that can be used to look up matches. All other translation functions use lookUp

A BioC annotation data package contains annotation data environments whose names are package name (e. g. hgu95av2) + element name (e. g. PMID). what must be one of the element names for the given data package.

getUniqAnnItem keeps track of the annotation elements that have one to one mappings.

Value

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

Author(s)

R. Gentleman

See Also

mget

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) ) {
      lookUp(gN, "hgu95av2", "SYMBOL")
      # Same as lookUp for SYMBOL except the return is a vector
      getSYMBOL(gN,"hgu95av2" )
      gg<- getGO(gN, "hgu95av2")
      lookUp(gg[[2]][[1]][["GOID"]], "GO", "TERM")
      # Same as lookUp for TERM
      getGOdesc(gg[[2]][[1]][["GOID"]], "ANY")
      # For BP only
      getGOdesc(gg[[2]][[1]][["GOID"]], "BP")
      getLL(gN, "hgu95av2")
      getPMID(gN, "hgu95av2")
  } else
   cat("could not run all examples\n")

[Package annotate version 1.8.0 Index]