viperRPT {viper} | R Documentation |
This function computes residual post-translational activity
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)
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 |
Matrix of RPT-activity values
data(bcellViper, package="bcellViper") vipermat <- viper(dset, regulon) rpt <- viperRPT(vipermat, dset) rpt[1:5, 1:5]