viper {viper} | R Documentation |
This function performs Virtual Inference of Protein-activity by Enriched Regulon analysis
viper(eset, regulon, dnull = NULL, pleiotropy = FALSE, nes = TRUE, method = c("none", "scale", "rank", "mad", "ttest"), bootstraps = 0, minsize = 25, adaptive.size = FALSE, eset.filter = TRUE, mvws = 1, pleiotropyArgs = list(regulators = 0.05, shadow = 0.05, targets = 10, penalty = 20, method = "adaptive"), cores = 1, verbose = TRUE)
eset |
ExpressionSet object or Numeric matrix containing the expression data or gene expression signatures, with samples in columns and genes in rows |
regulon |
Object of class regulon or list of objects of class regulon for metaVIPER analysis |
dnull |
Numeric matrix for the null model, usually generated by |
pleiotropy |
Logical, whether correction for pleiotropic regulation should be performed |
nes |
Logical, whether the enrichment score reported should be normalized |
method |
Character string indicating the method for computing the single samples signature, either scale, rank, mad, ttest or none |
bootstraps |
Integer indicating the number of bootstraps iterations to perform. Only the scale method is implemented with bootstraps. |
minsize |
Integer indicating the minimum number of targets allowed per regulon |
adaptive.size |
Logical, whether the weighting scores should be taken into account for computing the regulon size |
eset.filter |
Logical, whether the dataset should be limited only to the genes represented in the interactome #' @param mvws Number or vector indicating either the exponent score for the metaViper weights, or the inflection point and trend for the sigmoid function describing the weights in metaViper |
pleiotropyArgs |
list of 5 numbers for the pleotropy correction indicating: regulators p-value threshold, pleiotropic interaction p-value threshold, minimum number of targets in the overlap between pleiotropic regulators, penalty for the pleiotropic interactions and the method for computing the pleiotropy, either absolute or adaptive |
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 |
A matrix of inferred activity for each regulator gene in the network across all samples
data(bcellViper, package="bcellViper") d1 <- exprs(dset) res <- viper(d1, regulon) dim(d1) d1[1:5, 1:5] regulon dim(res) res[1:5, 1:5]