viper (version 1.6.0)

viperRPT: viperRPT

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]