signatureDistance: Signature Distance

In viper: 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]

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

          GSM44075  GSM44078  GSM44080  GSM44081  GSM44082
GSM44075 161.21596  44.89712  73.71824  70.82863  56.28180
GSM44078  44.89712 164.36313  35.61515  40.79263  42.74203
GSM44080  73.71824  35.61515 180.96934  79.44527  53.34445
GSM44081  70.82863  40.79263  79.44527 161.45038  54.23853
GSM44082  56.28180  42.74203  53.34445  54.23853 135.61676
          GSM44075  GSM44078  GSM44080  GSM44081  GSM44082
GSM44075 1.0000000 0.2757985 0.4308673 0.4390209 0.3792156
GSM44078 0.2757985 1.0000000 0.2062658 0.2504048 0.2849660
GSM44080 0.4308673 0.2062658 1.0000000 0.4640227 0.3369981
GSM44081 0.4390209 0.2504048 0.4640227 1.0000000 0.3651601
GSM44082 0.3792156 0.2849660 0.3369981 0.3651601 1.0000000
          GSM44075  GSM44078  GSM44080  GSM44081  GSM44082
GSM44075 0.0000000 0.7242015 0.5691327 0.5609791 0.6207844
GSM44078 0.7242015 0.0000000 0.7937342 0.7495952 0.7150340
GSM44080 0.5691327 0.7937342 0.0000000 0.5359773 0.6630019
GSM44081 0.5609791 0.7495952 0.5359773 0.0000000 0.6348399
GSM44082 0.6207844 0.7150340 0.6630019 0.6348399 0.0000000

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