euc: Euclidean distance

In bioDist: Different distance measures

Description

Calculate pairwise Euclidean distances and saves the result as a 'dist' object

Usage

euc(x, ...)

Arguments

x	n by p matrix or an object of a class that extends eSet; if x is a matrix, pairwise distances are calculated between the rows of a matrix. If x is an object of a class that extends eSet, the method makes use of the 'exprs' method and pairwise distances are calculated between samples(columns) if sample is TRUE
...	arguments passed to euc: 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 extends eSet, pairwise distances are calculated between samples(columns) if sample is TRUE ; default value is TRUE

Details

The method calculates pairwise euclidean distances, assuming that all samples have the same number of observations

Value

An object of class dist with the pairwise Euclidean distance between rows except in case of objects of class that extend eSet when sample is TRUE

Author(s)

Beiying Ding

See Also

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

Examples

 x <- matrix(rnorm(200), nrow = 5)
 euc(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  9.067795                              
3  8.613726  8.258428                    
4 10.802912  8.826257  7.930806          
5  9.794893  8.556541  8.893922  8.914316

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