geneset_overlap: geneset_overlap
In RITAN: Rapid Integration of Term Annotation and Network resources

Description Usage Arguments Value Examples

Return assymetric matrix of the fraction of genes shared between sets. E.G. The fraction of the first set that is "covered" by or "overlaps" the second set.

1	geneset_overlap(s1, s2 = s1, s.size = unlist(lapply(s1, length)))

`s1`	The first geneset
`s2`	the second geneset
`s.size`	Denominator used in each comparison. The default is to determint the lengths of elements in "s1"

results matrix of input gene list compared to active gene sets. Q value is calculated using entire group of active gene sets.

require(RITANdata)
r <- geneset_overlap( geneset_list$MSigDB_Hallmarks, geneset_list$NetPath_Gene_regulation )
heatmap(r, col = rev(gray(seq(0,1,length.out = 15))) )
summary(c(r))