viperSimilarity: VIPER similarity

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

Description

If ws is a single number, weighting is performed using an exponential function. If ws is a 2 numbers vector, weighting is performed with a symmetric sigmoid function using the first element as inflection point and the second as trend.

Usage

viperSimilarity(x, nn = NULL, ws = c(4, 2), method = c("two.sided",
  "greater", "less"))

Arguments

x	Numeric matrix containing the VIPER results with samples in columns and regulators in rows
nn	Optional number of top regulators to consider for computing the similarity
ws	Number indicating the weighting exponent for the signature, or vector of 2 numbers indicating the inflection point and the value corresponding to a weighting score of .1 for a sigmoid transformation, only used if nn is ommited
method	Character string indicating whether the most active (greater), less active (less) or both tails (two.sided) of the signature should be used for computing the similarity

Details

This function computes the similarity between VIPER signatures

Value

signatureDistance object

Examples

data(bcellViper, package="bcellViper")
dd <- viperSimilarity(exprs(dset))
dd[1:5, 1:5]
scale(dd)[1:5, 1:5]
as.matrix(as.dist(dd))[1:5, 1:5]

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