tau.dist: Kendall's tau correlational distance

In bioDist: Different distance measures

Description

Calculate pairwise Kendall's tau correlational distances, i.e. 1-TAU or 1-|TAU|, for all rows of the input matrix and return an instance of the dist class.

Usage

tau.dist(x, ...)

Arguments

x	n by p matrix or ExpressionSet; if x is an ExpressionSet, then the function uses its 'exprs' slot.
...	arguments passed to tau.dist: absif TRUE, then 1-|TAU| else 1-TAU; default is TRUE. diagif TRUE, then the diagonal of the distance matrix will be displayed; default is FALSE. upperif TRUE, then the upper triangle of the distance matrix will be displayed; default is FALSE. samplefor the ExpressionSet method: if TRUE (the default), then distances are computed between samples.

Details

Row-wise correlations are computed by calling the cor function with the appropriate arguments.

Value

One minus the row-wise Kendall's tau correlations are returned as an instance of the dist class. Note that this can be extremely slow for large data sets.

Author(s)

Beiying Ding

See Also

cor.dist, spearman.dist, euc, man, KLdist.matrix, KLD.matrix, mutualInfo

Examples

 x <- matrix(rnorm(200), nrow = 5)
 tau.dist(x)

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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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")'.

Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
          1         2         3         4
2 0.9461538                              
3 0.9769231 0.9333333                    
4 0.9564103 0.8717949 0.9333333          
5 0.9358974 0.8153846 0.9076923 0.9384615

bioDist documentation built on Nov. 8, 2020, 5:14 p.m.