computeMsigOverlap {vissE} | R Documentation

## Compute gene set overlap

### Description

Compute overlap between gene sets from a GeneSetCollection using the Jaccard index or the overlap coefficient. These values can then be used to compute a network of gene set overlaps.

### Usage

    computeMsigOverlap(
      msigGsc1,
      msigGsc2 = NULL,
      thresh = 0.15,
      measure = c("jaccard", "ovlapcoef")
    )

### Arguments

`msigGsc1` | a GeneSetCollection object.
`msigGsc2` | a GeneSetCollection object or NULL if pairwise overlaps are to be computed.
`thresh` | a numeric, specifying the threshold to discard pairs of gene sets.
`measure` | a character, specifying the similarity measure to use: `jaccard` for the Jaccard Index and `ovlapcoef` for the Overlap Coefficient.

### Value

a data.frame, containing the overlap structure of gene sets represented as a network in the simple interaction format (SIF).

### Examples

    data(hgsc)
    ovlap <- computeMsigOverlap(hgsc)

[Package vissE version 1.0.0 Index]