viper (version 1.6.0)

aREA: analytic Rank-based Enrichment Analysis

Description

This function performs wREA enrichment analysis on a set of signatues

Usage

aREA(eset, regulon, method = c("auto", "matrix", "loop"), minsize = 20, cores = 1, wm = NULL, verbose = FALSE)

Arguments

eset

Matrix containing a set of signatures, with samples in columns and traits in rows

regulon

Regulon object

method

Character string indicating the implementation, either auto, matrix or loop

minsize

Interger indicating the minimum allowed size for the regulons

cores

Integer indicating the number of cores to use (only 1 in Windows-based systems)

wm

Optional numeric matrix of weights (0; 1) with same dimension as eset

verbose

Logical, whether a progress bar should be shown

Value

List of two elements, enrichment score and normalized enrichment score