createOrthologousGeneSetList {RCAS} | R Documentation

## createOrthologousMsigdbDataset

### Description

Gene set annotations in public databases are usually geared towards human. This function is used to utilize human gene set annotations to create such gene sets for other species such as mouse, fly, and worm via orthologous relationships to human genes.

### Usage

    createOrthologousGeneSetList(referenceGeneSetList, refGenomeVersion = "hg19",
      targetGenomeVersion)

### Arguments

`referenceGeneSetList` | A named list of vectors where each vector consists of a set of Entrez gene ids (for instance, returned by `parseMsigdb` function
`refGenomeVersion` | Genome version of a reference species. (default:hg19)
`targetGenomeVersion` | Genome version of a target species. Available options are mm9, dm3, and ce10

### Value

A list of vectors where each vector consists of a set of Entrez gene ids

### Examples

    #Recommended gene sets (with Entrez Ids) from MSIGDB database can be downloaded
    #from \url{http://software.broadinstitute.org/gsea/msigdb/collections.jsp#C2}
    #Here we use built-in random gene sets to show how the function works
    data(geneSets)
    #Map the gene sets to a target genome (supported genomes: mm9, dm3, or ce10)
    orthGeneSets <- createOrthologousGeneSetList(
                                 referenceGeneSetList = geneSets,
                                 refGenomeVersion = 'hg19',
                                 targetGenomeVersion = 'mm9'
                                 )

[Package RCAS version 1.6.0 Index]