getSYMBOL: 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)
getEG(x, data)
getGO(x, data)
getPMID(x, data)
getGOdesc(x, which)
lookUp(x, data, what, load = FALSE)
getUniqAnnItem()

Arguments

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 categories of interest

load

A logical value indicating whether to attempt to load the required annotation data package if it isn't already loaded.

Value

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

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 getEG 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 x contains GO identifiers (not manufacturer identifiers) and the output is a list of GOTerms objects, if which specifies some subset of the ontologies (MF, BP or CC) then only terms for that ontology are retained.

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.

Examples

Run this code

  library("hgu95av2.db")
  library("GO.db")

  data(sample.ExpressionSet)
  gN <- featureNames(sample.ExpressionSet)[100:105]
  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")
  getEG(gN, "hgu95av2")
  getPMID(gN, "hgu95av2")