| 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")