pairwiseSetOverlap: All Pairwise Comparisons Between Gene Sets of Two Libraries

In MaayanLab/genesetr: Manipulate, Test, and Visualize Gene Set Overlaps

Description

All Pairwise Comparisons Between Gene Sets of Two Libraries

Usage

pairwiseSetOverlap(lib1, lib2, background = NULL, method = "FET")

Arguments

lib1	A library of gene sets in List, LongDF or Mat format.
lib2	A library of gene sets in List, LongDF or Mat format.
background	The size of the "universe" of genes to use in building contingency tables from pairwise intersections of gene sets in the two libraries. Default is NULL– background will be computed as the size of the union of unique genes in lib1 and lib2.
method	Metric by which to assess gene set association. Options are "FET" and "OR".

Value

A data frame with all pairs of genesets and association metrics

Examples

#load example gene set libraries
data("encode_example", "chea_example")
intersects = pairwiseSetOverlap(encode_example, chea_example)

MaayanLab/genesetr documentation built on Aug. 14, 2019, 12:20 p.m.