kmeans2: K-means clustering for gene expression data

Description Usage Arguments Value Author(s) See Also Examples

View source: R/kmeans2.R

Description

This function is a wrapper function for kmeans of the e1071 package. It performs hard clustering of genes based on their expression values using the k-means algorithm.

Usage

1
kmeans2(eset,k,iter.max=100)

Arguments

eset

object of the class ExpressionSet.

k

number of clusters.

iter.max

maximal number of iterations.

Value

An list of clustering components (see kmeans).

Author(s)

Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)

See Also

kmeans

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
if (interactive()){
data(yeast)
# Data pre-processing
yeastF <- filter.NA(yeast)
yeastF <- fill.NA(yeastF)
yeastF <- standardise(yeastF)

# K-means clustering and visualisation
kl <- kmeans2(yeastF,k=20)
kmeans2.plot(yeastF,kl=kl,mfrow=c(2,2))
}

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: e1071
Warning message:
no DISPLAY variable so Tk is not available 

Mfuzz documentation built on Nov. 1, 2018, 5:03 a.m.