computeGeneSetsOverlap {GSVA} | R Documentation

## Compute gene-sets overlap

### 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)))

[Package GSVA version 1.28.0 Index]