bicluster: Extract a bicluster

In BicARE: Biclustering Analysis and Results Exploration

Description

Extract a bicluster from an object of class biclustering

Usage

bicluster(biclustering, k, graph=TRUE)

Arguments

biclustering	an object of class "biclustering" created by function FLOC
k	the number of the bicluster considered in the "biclustering" object
graph	boolean, indicating whether the graph should be plotted or not

Value

Returns the bicluster as a matrix with the genes on rows and the samples on columns. Result matrix is of class "bicluster". The "graph" option allows to plot the expression profiles of the genes across the conditions in the bicluster.

Author(s)

Pierre Gestraud

Examples

### extract the first bicluster
data(sample.biclustering)
sample.biclustering
bic <- bicluster(sample.biclustering, 1, graph=TRUE)
plot(bic)

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: multtest
Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

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

    addNode


Call : 
FLOC(Data = sample.bicData, k = 10, pGene = 0.3, pSample = 0.5, 
    r = 0.025, N = 8, M = 8, t = 1000)

Parameters :
 number of biclusters :  10
 residu threshold :  0.025
 gene initial probability :  0.3
 sample initial probability :  0.5
 number of iterations :  1000
 date :  Mon Jun  9 17:41:43 2008
Biclusters : 
         residue volume genes conditions     rowvar
 [1,] 0.02524415    576    72          8 0.05902643
 [2,] 0.02492381    512    64          8 0.06630674
 [3,] 0.02554222    680    85          8 0.03228695
 [4,] 0.02488630    608    76          8 0.04896948
 [5,] 0.02697185    560    70          8 0.05048769
 [6,] 0.02591990    544    68          8 0.08208585
 [7,] 0.02542855    472    59          8 0.04320073
 [8,] 0.02884928    560    70          8 0.06956491
 [9,] 0.02649677    560    70          8 0.04285773
[10,] 0.02474255    632    79          8 0.04915166

BicARE documentation built on Nov. 8, 2020, 7:47 p.m.