minSetSize-methods: GeneSetCollection length filtering

Description

This function filteres a GeneSetCollection by removing all contained GeneSets that do not include at least the user-specified number of genes also found in the user-specified universe.

Usage

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## S4 method for signature 'CMAPCollection'
minSetSize(sets, universe=NULL, min.members = 5)

Arguments

sets

A CMAPCollection object.

universe

Optional character vector of gene identfiers to be considered as the universe. Only geneIds included in the universe will count toward the gene set membership counts. If 'NULL' (default), all featureNames of the CMAPCollection will be considered.

min.members

Number of genes (in the univerese) a gene set needs to contain to be retained.

Value

A CMAPCollection with all gene sets containing more than the specified number of members.

Author(s)

Thomas Sandmann

Examples

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data(gCMAPData)
gene.set.collection <- induceCMAPCollection(gCMAPData, "z", higher=2, lower=-2)

minSetSize(gene.set.collection, min.members=100)

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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