viper (version 1.6.0)

viperSimilarity: VIPER similarity

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, 1), 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, 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

Value

signatureDistance object

Details

This function computes the similarity between VIPER signatures

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]