Description Usage Arguments Value Author(s) See Also Examples
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.
1 | kmeans2(eset,k,iter.max=100)
|
eset |
object of the class ExpressionSet. |
k |
number of clusters. |
iter.max |
maximal number of iterations. |
An list of clustering components (see
kmeans
).
Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)
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))
}
|
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
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Loading required package: e1071
Warning message:
no DISPLAY variable so Tk is not available
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