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)
    getEG(x, data)
    getGO(x, data)
    getPMID(x, data)
    getGOdesc(x, which)
    lookUp(x, data, what, load = FALSE)
    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 categories of interest
`load` | A logical value indicating whether to attempt to load the required annotation data package if it isn't already loaded.

### 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.

### Value

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

### Author(s)

R. Gentleman

### See Also

`mget`

### Examples

      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")

[Package annotate version 1.20.1 Index]