aracne2regulon: Regulon object generation from ARACNe results

Description Usage Arguments Value See Also Examples

View source: R/aracne.r

Description

This function generates a regulon object from ARACNe results and the corresponding expression dataset

Usage

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aracne2regulon(afile, eset, 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

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

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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:BiocGenericsThe following objects are masked frompackage:parallel:

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

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage: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.