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(sample.exprSet.1)
      gN <- geneNames(sample.exprSet.1)[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 1.10.0 Index]