geneset_overlap: geneset_overlap

In MTZimmer/RITAN: Rapid Integration of Term Annotation and Network resources

Description

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.

Usage

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

Arguments

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"

Value

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

Examples

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))

MTZimmer/RITAN documentation built on Feb. 21, 2020, 7:09 a.m.