viper (version 1.6.0)

signatureDistance: Signature Distance

Description

This function computes the similarity between columns of a data matrix

Usage

signatureDistance(dset1, dset2 = NULL, nn = NULL, groups = NULL, scale. = TRUE, two.tails = TRUE, ws = 2)

Arguments

dset1

Dataset of any type in matrix format, with features in rows and samples in columns

dset2

Optional Dataset. If provided, distance between columns of dset and dset2 are computed and reported as rows and columns, respectively; if not, distance between all possible pairs of columns from dset are computed

nn

Optional size for the signature, default is either the full signature or 10 percent of it, depending or whether ws=0 or not

groups

Optional vector indicating the group ID of the samples

scale.

Logical, whether the data should be scaled

two.tails

Logical, whether a two tails, instead of 1 tail test should be performed

ws

Number indicating the exponent for the weighting the signatures, the default of 0 is uniform weighting, 1 is weighting by SD

Value

Object of class signatureDistance as a matrix of normalized enrichment scores

Examples

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