aracne2regulon4cnv: Regulon object generation from ARACNe results corrected by...

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

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)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Loading the dataset...
Generating the regulon objects...
number of iterations= 301 
mu: -0.328177385605993, 0, 0.386904997063304. sigma: 0.116291346506325, 0.195256830738426, 0.12153218588778
Object of class regulon with 20 regulators, 3758 targets and 6013 interactions

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