characteriseGeneset {vissE} | R Documentation |
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.
characteriseGeneset( gs, thresh = 0.2, measure = c("ovlapcoef", "jaccard"), gscolcs = c("h", "c2", "c5") )
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:
|
gscolcs |
a character, listing the MSigDB collections to use as a
background (defaults to h, c2, and c5). Collection types can be retrieved
using |
an igraph object, containing gene sets that are similar to the query set. The network contains relationships between results of the query too.
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)