characteriseGeneset {vissE}R Documentation

Functionally characterise a list of genes

Description

This function can be used to perform a network-based enrichment analysis of a list of genes. The list of genes are characterised based on their similarity with gene sets from the MSigDB. A network of similar gene sets is retrieved using this function.

Usage

characteriseGeneset(
  gs,
  thresh = 0.2,
  measure = c("ovlapcoef", "jaccard"),
  gscolcs = c("h", "c2", "c5")
)

Arguments

gs

a GeneSet object, representing the list of genes that need to be characterised.

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.

gscolcs

a character, listing the MSigDB collections to use as a background (defaults to h, c2, and c5). Collection types can be retrieved using msigdb::listCollections().

Value

an igraph object, containing gene sets that are similar to the query set. The network contains relationships between results of the query too.

Examples

library(GSEABase)
data(hgsc)

#create a geneset using one of the Hallmark gene sets
mySet <- GeneSet(
  geneIds(hgsc[[2]]),
  setName = 'MySet',
  geneIdType = SymbolIdentifier()
)


#characterise the custom gene set
ig <- characteriseGeneset(mySet)
plotMsigNetwork(ig)



[Package vissE version 1.0.0 Index]