filterGeneSets: Filter gene sets

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

Description

Filters gene sets through a given minimum and maximum set size.

Usage

## S4 method for signature 'list'
filterGeneSets(gSets, min.sz=1, max.sz=Inf)
## S4 method for signature 'GeneSetCollection'
filterGeneSets(gSets, min.sz=1, max.sz=Inf)

Arguments

gSets	Gene sets given either as a list or a GeneSetCollection object.
min.sz	Minimum size.
max.sz	Maximum size.

Details

This function filters the input gene sets according to a given minimum and maximum set size.

Value

A collection of gene sets that meet the given minimum and maximum set size.

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

computeGeneSetsOverlap

Examples

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

filterGeneSets(geneSets, min.sz=5)

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