tmodLEA: Leading Edge Analysis

In tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Leading Edge Analysis

Description

For each module, return a list of genes on the leading edge

Usage

tmodLEA(l, modules, mset = "all", nodups = TRUE, filter = FALSE)

Arguments

l	list of genes
modules	character vector of module IDs for which to run the LEA
mset	Which module set to use. Either a character vector ("LI", "DC" or "all", default: LI) or an object of class tmod
nodups	Remove duplicate gene names in l and corresponding rows from ranks
filter	Remove gene names which have no module assignments

Details

Given a vector of ordered gene identifiers and a vector of module IDs, for each module, return the genes which are on the up-slope of the GSEA-style evidence plot. That is, return the genes that are driving the enrichment.

tmod documentation built on March 31, 2023, 9 p.m.