groupPwea3: Proportionally Weighted Enrichment Analysis for gene-set...

In viper: Virtual Inference of Protein-activity by Enriched Regulon analysis

Description

This function performs a Proportionally Weighted Enrichment Analysis on groups of gene-sets

Usage

groupPwea3(rlist, groups, nullpw = NULL, alternative = c("two.sided",
  "less", "greater"), per = 0, minsize = 5, cores = 1,
  verbose = TRUE)

Arguments

rlist	Named vector containing the scores to rank the expression profile or matrix where columns contains bootstraped signatures
groups	List of gene-sets (regulons), each component is a list of two vectors: TFmode containing the TFMoA index (-1; 1) and likelihood containing the interaction relative likelihood
nullpw	Numerical matrix representing the null model, with genes as rows (geneID as rownames) and permutations as columns
alternative	Character string indicating the alternative hypothesis, either two.sided, greater or less
per	Integer indicating the number of permutations for the genes in case "nullpw" is ommited
minsize	Integer indicating the minimum size for the regulons
cores	Integer indicating the number of cores to use (only 1 in Windows-based systems)
verbose	Logical, whether progression messages should be printed in the terminal

Value

A list containing four matrices:

es

Enrichment score

nes

Normalized Enrichment Score

size

Regulon size

p.value

Enrichment p.value

viper documentation built on Nov. 8, 2020, 7:37 p.m.