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) lookUp(x, data, what) getUniqAnnItem()
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 |
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.
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) ) { 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")