cor.dist: Pearson correlational distance

In bioDist: Different distance measures

Description

Calculate pairwise Pearson correlational distances, i.e. 1-COR or 1-|COR|, and saves as a 'dist' object

Usage

cor.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 cor.dist: absif TRUE, then 1-|COR| else 1-COR, 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 objects of classes that extend eSet: if TRUE, then distances are computed between samples(columns) , otherwise, they are computed between features(rows).

Details

The cor function is used to compute the pairwise distances between rows of an input matrix, except if the input is an object of a class that extends eSet and sample is TRUE.

Value

Pairwise Pearson correlational distance object

Author(s)

Beiying Ding

See Also

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

Examples

 x <- matrix(rnorm(200), nrow = 5)
 cor.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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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 0.9467802                              
3 0.7721057 0.9792828                    
4 0.9643140 0.9028227 0.7762623          
5 0.8803607 0.9169750 0.6741129 0.8197732

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