createOrthologousGeneSetList: createOrthologousMsigdbDataset

Description Usage Arguments Value Examples

View source: R/enrichment_analysis.R

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

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createOrthologousGeneSetList(referenceGeneSetList, refSpecies = "hsapiens",
  targetSpecies)

Arguments

referenceGeneSetList

A named list of vectors where each vector consists of a set of Entrez gene ids (for instance, returned by parseMsigdb function

refSpecies

Reference species (e.g. hsapiens)

targetSpecies

Target species (e.g. mmusculus)

Value

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

Examples

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#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,
                             refSpecies = 'hsapiens',
                             targetSpecies = 'mmusculus'
                             )

RCAS documentation built on Nov. 1, 2018, 2:54 a.m.