pruneRegulon {viper}R Documentation

Prune Regulons

Description

This function limits the maximum size of the regulons

Usage

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

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

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)

[Package viper version 1.18.1 Index]