viper (version 1.6.0)

aracne2regulon4cnv: Regulon object generation from ARACNe results corrected by cnv

Description

This function generates a regulon object from ARACNe results and the corresponding expression dataset when correction for CNV have been applied

Usage

aracne2regulon4cnv(afile, eset, regeset, gene = FALSE, format = c("adj", "3col"), verbose = TRUE)

Arguments

afile

Character string indicating the name of the ARACNe network file

eset

Either a character string indicating the name of the expression-dataset file, a ExpressionSet object or a gene expression matrix with genes (probes) in rows and samples in columns, where the expression was corrected by CNV

regeset

Either a character string indicating the name of the expression-dataset file, a ExpressionSet object or a gene expression matrix with genes (probes) in rows and samples in columns

gene

Logical, whether the probes should be collapsed at the gene level

format

Character string, indicating the format of the aracne file, either adj for adjacency matrixes generated by aracne, or 3col when the interactome is represented by a 3 columns text file, with regulator in the first column, target in the second and mutual information in the third column

verbose

Logical, whether progression messages should be printed in the terminal.

Value

Regulon object

See Also

msviper, viper

Examples

data(bcellViper, package="bcellViper")
adjfile <- file.path(find.package("bcellViper"), "aracne", "bcellaracne.adj")
regul <- aracne2regulon(adjfile, dset)
print(regul)