aracne2regulon4cnv {viper} | R Documentation |
This function generates a regulon object from ARACNe results and the corresponding expression dataset when correction for CNV have been applied
aracne2regulon4cnv(afile, eset, regeset, gene = FALSE, format = c("adj", "3col"), verbose = TRUE)
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. |
Regulon object
data(bcellViper, package="bcellViper") adjfile <- file.path(find.package("bcellViper"), "aracne", "bcellaracne.adj") regul <- aracne2regulon(adjfile, dset) print(regul)