membership: Calculating of membership values for new data based on...

In Mfuzz: Soft clustering of time series gene expression data

Description

Function that calculates the membership values of genes based on provided data and existing clustering

Usage

membership(x,clusters,m)

Arguments

x	expression vector or expression matrix
clusters	cluster centroids from existing clustering
m	fuzzification parameter

Value

Matrix of membership values for new genes

Note

This function calculates membership values for new data based on existing cluster centroids and fuzzification parameter. It can be useful, for instance, when comparing two time series, to assess whether the same gene in the different time series changes its cluster association.

Author(s)

Matthias E. Futschik (http://www.sysbiolab.eu)

Examples

if (interactive()){
 data(yeast)
 yeastF <- filter.NA(yeast)
 yeastF <- fill.NA(yeastF) # for illustration only; rather use knn method
 yeastF <- standardise(yeastF)
 
 cl <- mfuzz(yeastF,c=20,m=1.25)

 m <- 1.25
 clusters <- cl[[1]]
 x <- matrix(rnorm(2*17),nrow=2) # new expression matrix with two genes 
 mem.tmp <- membership(x,clusters=clusters,m=m) #membership values  
}

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. 8, 2020, 5:22 p.m.