signatureDistance: Signature Distance

In chrischen1/viper_copy: Virtual Inference of Protein-activity by Enriched Regulon analysis

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]

chrischen1/viper_copy documentation built on May 13, 2019, 6:52 p.m.