acore: Extraction of alpha cores for soft clusters

Description Usage Arguments Value Author(s) Examples

View source: R/acore.R

Description

This function extracts genes forming the alpha cores of soft clusters

Usage

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acore(eset,cl,min.acore=0.5)

Arguments

eset

object of the class ExpressionSet.

cl

An object of class flcust as produced by mfuzz.

min.acore

minimum membership values of gene belonging to the cluster core.

Value

The function produces an list of alpha cores including genes and their membership values for the corresponding cluster.

Author(s)

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

Examples

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if (interactive()){
### Data loaing and pre-processing
 data(yeast) # data set includes 17 measurements
 yeastF <- filter.NA(yeast) 
 yeastF <- fill.NA(yeastF)
 yeastF <- standardise(yeastF)

### Soft clustering and visualisation
cl <- mfuzz(yeastF,c=20,m=1.25)
acore.list <- acore(yeastF,cl=cl,min.acore=0.7)
 }

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.