geneset_overlap: geneset_overlap

Description Usage Arguments Value Examples

View source: R/lib_enrichment.R

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

1
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

1
2
3
4
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 Oct. 11, 2018, 10:17 a.m.