spearman.dist: Spearman correlational distance

In bioDist: Different distance measures

Description

Calculate pairwise Spearman correlational distances, i.e. 1-SPEAR or 1-|SPEAR|, for all rows of a matrix and return a dist object.

Usage

spearman.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 spearman.dist: absif TRUE, then 1-|SPEAR| else 1-SPEAR; 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

We call cor with the appropriate arguments to compute the row-wise correlations.

Value

One minus the Spearman correlation, between rows of x, are returned, as an instance of the dist class.

Author(s)

Beiying Ding

See Also

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

Examples

 x <- matrix(rnorm(200), nrow = 5)
 spearman.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 0.7564728                              
3 0.7859287 0.8879925                    
4 0.8943715 0.8949343 0.9923077          
5 0.8844278 0.8943715 0.9924953 0.7429644

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