pruneRegulon: Prune Regulons

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

Description

This function limits the maximum size of the regulons

Usage

pruneRegulon(regulon, cutoff = 50, adaptive = TRUE,
  eliminate = FALSE, wm = NULL)

Arguments

regulon	Object of class regulon
cutoff	Number indicating the maximum size for the regulons (maximum number of target genes)
adaptive	Logical, whether adaptive size should be used (i.e. sum(likelihood^2))
eliminate	Logical whether regulons smalles than cutoff should be eliminated
wm	Optional numeric vector of weights (0; 1) for the genes

Value

Prunned regulon

See Also

viper, msviper

Examples

data(bcellViper, package="bcellViper")
hist(sapply(regulon, function(x) sum(x$likelihood)/max(x$likelihood)), nclass=20)
preg <- pruneRegulon(regulon, 400)
hist(sapply(preg, function(x) sum(x$likelihood)/max(x$likelihood)), nclass=20)

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