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

Description Usage Arguments Value

Description

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

Usage

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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


chrischen1/viper_copy documentation built on May 13, 2019, 6:52 p.m.