modOverlaps: Calculate overlaps of the modules

Description Usage Arguments Details

View source: R/modstats.R

Description

Calculate overlaps of the modules

Usage

1
modOverlaps(modules, mset = NULL, stat = "jaccard")

Arguments

modules

either a character vector with module IDs from mset, or a list which contains the module members

mset

Which module set to use. Either a character vector ("LI", "DC" or "all", default: LI) or an object of class tmod (see "Custom module definitions" below)

stat

Type of statistics to return. "number": number of common genes (default); "jaccard": Jaccard index; "soerensen": Soerensen-Dice coefficient; "overlap": Szymkiewicz-Simpson coefficient.

Details

For a set of modules (aka gene sets) determine the similarity between these. You can run modOverlaps either on a character vector of module IDs or on a list. In the first case, the module elements are taken from 'mset', and if that is NULL, from the default tmod module set.

Alternatively, you can provide a list in which each element is a character vector. In this case, the names of the list are the module IDs, and the character vectors contain the associated elements.

The different statistics available are: * "number": total number of common genes (size of the overlap) * "jaccard": Jaccard index, i.e. \frac{|A \cap B|}{|A \cup B|} (number of common elements divided by the total number of unique elements); * "soerensen": Soerensen-Dice coefficient, defined as \frac{2 \cdot |A \cap B|}{|A| + |B|} (number of common elements divided by the average size of both gene sets) * "overlap": Szymkiewicz-Simpson coefficient, defined as \frac{|A \cap B|}{\min(|A|, |B|)} (number of common elements divided by the size of the smaller gene set)


tmod documentation built on Oct. 23, 2020, 6:12 p.m.