getSYMBOL {annotate} | R Documentation |
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.
getSYMBOL(x, data) getLL(x, data) getGO(x, data) getPMID(x, data) getGOdesc(x, which=c("MF","BP","CC") ) contents(object)
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 |
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.
Either a vector or a list depending on whether multiple values per input are possible.
R. Gentleman
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")