gsaTranslateGmt: GSA Translate GMT
In bernau/survHDExtra: Addtitional Features for package survHD

Description Usage Arguments Details Value Author(s) See Also Examples

Converts a GMT file so that symbols match rownames of X.

## S4 method for signature 'gsagenesets,matrix,character'
gsaTranslateGmt(gmt, X, genes)
## S4 method for signature 'gsagenesets,ExpressionSet,character'
gsaTranslateGmt(gmt, X, genes)
## S4 method for signature 'gsagenesets,data.frame,character'
gsaTranslateGmt(gmt, X, genes)

`gmt`	An object of class `gsagenesets` or a list of gene sets.
`X`	An object of class `ExpressionSet`, matrix or data.frame.
`genes`	An `character` vector with the gene names of X.

Can be used to translate gene sets, for example from official gene symbols to manufacturer probe ids.

An object of class gsagenesets.

Markus Riester markus@jimmy.harvard.edu, Levi Waldron lwaldron@hsph.harvard.edu, Christoph Bernau bernau@ibe.med.uni-muenchen.de

gsaReadGmt, gsaTranslateGmt

    library(survHD)
    library(survHDExtra)
    library(hu6800.db)
    library(annotate)

    data(beer.exprs)
    data(beer.survival)
    gmt <- gsaReadGmt(system.file("extdata/ovarian_gene_signatures.gmt", package = "survHD"))
    # the Gmt file contains gene symbols, so we translate it to Affymetrix 
    genes <- getSYMBOL(rownames(beer.exprs), "hu6800")
    gmt.affy <- gsaTranslateGmt(gmt, beer.exprs, genes)