computeGeneSetsOverlap: Compute gene-sets overlap

In GSVA: Gene Set Variation Analysis for microarray and RNA-seq data

Description

Calculates the overlap among every pair of gene-sets given as input.

Usage

## S4 method for signature 'list,character'
computeGeneSetsOverlap(gSets, uniqGenes, min.sz=1, max.sz=Inf)
## S4 method for signature 'list,ExpressionSet'
computeGeneSetsOverlap(gSets, uniqGenes, min.sz=1, max.sz=Inf)
## S4 method for signature 'GeneSetCollection,character'
computeGeneSetsOverlap(gSets, uniqGenes, min.sz=1, max.sz=Inf)
## S4 method for signature 'GeneSetCollection,ExpressionSet'
computeGeneSetsOverlap(gSets, uniqGenes, min.sz=1, max.sz=Inf)

Arguments

gSets	Gene sets given either as a list or a GeneSetCollection object.
uniqGenes	Vector of unique genes to be considered when calculating the overlaps.
min.sz	Minimum size.
max.sz	Maximum size.

Details

This function calculates the overlap between every pair of gene sets of the input argument gSets. Before this calculation takes place, the gene sets in gSets are firstly filtered to discard genes that do not match to the identifiers in uniqGenes. Secondly, they are further filtered to meet the minimum and/or maximum size specified with the arguments min.sz and max.sz. The overlap between two gene sets is calculated as the number of common genes between the two gene sets divided by the smallest size of the two gene sets.

Value

A gene-set by gene-set matrix of the overlap among every pair of gene sets.

Author(s)

J. Guinney

References

Hänzelmann, S., Castelo, R. and Guinney, J. GSVA: Gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics, 14:7, 2013.

See Also

filterGeneSets

Examples

geneSets <- list(set1=as.character(1:4), set2=as.character(4:10))

computeGeneSetsOverlap(geneSets, unique(unlist(geneSets)))

GSVA documentation built on Feb. 11, 2021, 2:02 a.m.