getIncidence: Determines the incidence of a gene set in a list of genes.

In npGSEA: Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)

Description

Calculates the incidence of a gene set in an experiment

Usage

  getIncidence(universeIDs, set)

Arguments

universeIDs	A vector containing the list of possible gene ids in the universe (or experiment).
set	A GeneSet object containing a set of genes of interest

Details

getIncidence returns an incidence vector of the location of the genes within a gene set in a list of genes in an experiment and vise-versa.

Value

A list of inSet and inExp. inSet is a vector with the same length as universeIDs. Each value of inSet is 1 if the gene is in the set and 0 otherwise. inExp is a vector with the same length as geneIds(set), the number of genes in the set. Each value of inExp is 1 if the gene is in universeIDs and 0 otherwise.

Author(s)

Jessica L. Larson and Art Owen

References

Jessica L Larson and Art B Owen: Moment based gene set tests. BMC Bioinformatics 2015, 16:132. http://www.biomedcentral.com/1471-2105/16/132

Examples

    geneSetABC15 <- GeneSet(geneIds=letters[1:15], setName="setABC15")
    getIncidence(letters, geneSetABC15)

npGSEA documentation built on Nov. 8, 2020, 6:49 p.m.