viper (version 1.6.0)

bootstrapViper: bootstrapsViper

Description

This function performs a viper analysis with bootstraps

Usage

bootstrapViper(eset, regulon, nes = TRUE, bootstraps = 10, cores = 1, verbose = TRUE)

Arguments

eset

ExpressionSet object or Numeric matrix containing the expression data, with samples in columns and genes in rows

regulon

Object of class regulon

nes

Logical, whether the enrichment score reported should be normalized

bootstraps

Integer indicating the number of bootstraps iterations to perform. Only the scale method is implemented with bootstraps.

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 a matrix of inferred activity for each regulator gene in the network across all samples and the corresponding standard deviation computed from the bootstrap iterations.

See Also

viper

Examples

data(bcellViper, package="bcellViper")
d1 <- exprs(dset)
res <- viper(d1[, 1:50], regulon, bootstraps=10) # Run only on 50 samples to reduce computation time
dim(d1)
d1[1:5, 1:5]
regulon
dim(res$nes)
res$nes[1:5, 1:5]
res$sd[1:5, 1:5]