computeGeneSetsOverlap: Compute gene-sets overlap

In rcastelo/GSVA: Gene Set Variation Analysis for Microarray and RNA-Seq Data

Compute gene-sets overlap

Description

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

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 minSize and maxSize. 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.

Usage

## S4 method for signature 'list,character'
computeGeneSetsOverlap(gSets, uniqGenes, minSize = 1, maxSize = Inf)

## S4 method for signature 'list,ExpressionSet'
computeGeneSetsOverlap(gSets, uniqGenes, minSize = 1, maxSize = Inf)

## S4 method for signature 'GeneSetCollection,character'
computeGeneSetsOverlap(gSets, uniqGenes, minSize = 1, maxSize = Inf)

## S4 method for signature 'GeneSetCollection,ExpressionSet'
computeGeneSetsOverlap(gSets, uniqGenes, minSize = 1, maxSize = 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.
minSize	Minimum size.
maxSize	Maximum size.

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)))

rcastelo/GSVA documentation built on Dec. 17, 2024, 4:51 p.m.