viperRPT: viperRPT

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

Description

This function computes residual post-translational activity

Usage

viperRPT(vipermat, expmat, weights = matrix(1, nrow(vipermat),
  ncol(vipermat), dimnames = list(rownames(vipermat), colnames(vipermat))),
  method = c("spline", "lineal", "rank"), robust = FALSE, cores = 1)

Arguments

vipermat	Numeric matrix containing the viper protein activity inferences
expmat	Numeric matrix or expressionSet containing the expression data
weights	List of numeric matrix of sample weights
method	Character string indicating the method to use, either rank, lineal or spline
robust	Logical, whether the contribution of outliers is down-weighted by using a gaussian kernel estimate for the join probability density
cores	Integer indicating the number of cores to use

Value

Matrix of RPT-activity values

See Also

viper

Examples

data(bcellViper, package="bcellViper")
vipermat <- viper(dset, regulon)
rpt <- viperRPT(vipermat, dset)
rpt[1:5, 1:5]

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