viper: VIPER

In chrischen1/viper_copy: Virtual Inference of Protein-activity by Enriched Regulon analysis

Description

This function performs Virtual Inference of Protein-activity by Enriched Regulon analysis

Usage

viper(eset, regulon, dnull = NULL, pleiotropy = FALSE, nes = TRUE,
  method = c("scale", "rank", "mad", "ttest", "none"), bootstraps = 0,
  minsize = 25, adaptive.size = FALSE, eset.filter = TRUE,
  pleiotropyArgs = list(regulators = 0.05, shadow = 0.05, targets = 10,
  penalty = 20, method = "adaptive"), cores = 1, verbose = TRUE)

Arguments

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
dnull	Numeric matrix for the null model, usually generated by nullTtest
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
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

Value

A matrix of inferred activity for each regulator gene in the network across all samples

See Also

msviper

Examples

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]

chrischen1/viper_copy documentation built on May 13, 2019, 6:52 p.m.