modGroups: Find group of modules

In tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Find group of modules

Description

Find group of modules based on shared genes

Usage

modGroups(modules, mset = NULL, min.overlap = 2, stat = "number")

Arguments

modules	Either a list of modules or character vector.
mset	Which module set to use. Either a character vector ("LI", "DC" or "all", default: all) or an object of class tmod (see "Custom module definitions" below)
min.overlap	Minimum number of overlapping items if stat == number, minimum jaccard index if stat == jaccard etc.
stat	Type of statistics to return. "jaccard": Jaccard index (default); "number": number of common genes; "soerensen": Soerensen-Dice coefficient; "overlap": Szymkiewicz-Simpson coefficient.

Details

Split the modules into groups based on the overlapping items.

The first argument, modules, is either a character vector of module identifiers from 'mset' (NULL mset indicates the default mset of tmod) or a list. If it is a list, then each element is assumed to be a character vector with module IDs.

Examples

mymods <- list(A=c(1, 2, 3), B=c(2, 3, 4, 5), C=c(5, 6, 7))
modGroups(mymods)

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