connectivity_score: Broad CMAP gene set enrichment metrics

In jzsh2000/jzshr: jzsh2000's R Code

Description

A method for computing Broad CMAP connectivity scores. This method is a kind of gene set enrichment analysis, it's initially designed for microarray samples, but could also applied to RNA-seq data. To use this method, we need a expression matrix and two corresponding gene sets.

Usage

connectivity_score(data.matrix, id.up, id.down)

Arguments

data.matrix	the gene expression matrix
id.up	first gene set, usually the up-regulated genes in a cell line
id.down	second gene set, usually the down-regulated genes in a cell line

References

http://portals.broadinstitute.org/cmap/help_topics_linkified.jsp#connectivity score

See Also

connectivity_score

jzsh2000/jzshr documentation built on May 20, 2019, 6:29 a.m.