mestimate: Estimate for optimal fuzzifier m

In Mfuzz: Soft clustering of time series gene expression data

Description

This function estimates an optimal setting of fuzzifier m

Usage

mestimate(eset)

Arguments

eset	object of class “ExpressionSet”

Details

Schwaemmle and Jensen proposed an method to estimate of m, which was motivated by the evaluation of fuzzy clustering applied to randomized datasets. The estimated m should give the minimum fuzzifier value which prevents clustering of randomized data.

Value

Estimate for optimal fuzzifier.

Author(s)

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

References

Schwaemmle and Jensen, Bioinformatics,Vol. 26 (22), 2841-2848, 2010

Examples

if (interactive()){
data(yeast)
# Data pre-processing
yeastF <- filter.NA(yeast)
yeastF <- fill.NA(yeastF)
yeastF <- standardise(yeastF)

#### parameter selection

#### parameter selection
# For fuzzifier m, we could use mestimate
m1 <- mestimate(yeastF)
m1 # 1.15

cl <- mfuzz(yeastF,c=20,m=m1)
mfuzz.plot(yeastF,cl=cl,mfrow=c(4,5))
}

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: e1071

Attaching package: 'DynDoc'

The following object is masked from 'package:BiocGenerics':

    path

Warning message:
no DISPLAY variable so Tk is not available 

Mfuzz documentation built on Nov. 8, 2020, 5:22 p.m.