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