BCXmotifs: The Xmotifs Bicluster algorithm

In biclust: BiCluster Algorithms

Description

Performs XMotifs Biclustering based on the framework by Murali and Kasif (2003). Searches for a submatrix where each row as a similar motif through all columns. The Algorihm needs a discret matrix to perform.

Usage

## S4 method for signature 'matrix,BCXmotifs'
biclust(x, method=BCXmotifs(), ns=10, nd=10, sd=5, alpha=0.05, number=100)

Arguments

x	Data Matrix.
method	Here BCXmotifs, to perform Xmotifs algorithm
ns	Number of columns choosen.
nd	Number of repetitions.
sd	Sample size in repetitions.
alpha	Scaling factor for column result.
number	Number of bicluster to be found.

Value

Returns an object of class Biclust.

Extends

Class "BiclustMethod", directly.

Author(s)

Sebastian Kaiser [e-mail]

References

Murali, T. & Kasif, S. Extracting Conserved Gene Expression Motifs from Gene Expression Data Pacific Symposium on Biocomputing, sullivan.bu.edu, 2003, 8, 77-88

See Also

biclust, Biclust

Examples

data(BicatYeast)
x<-discretize(BicatYeast)
res <- biclust(x, method=BCXmotifs(), ns=20, nd=20, sd=5, alpha=0.01, number=10)
res

Example output

Loading required package: MASS
Loading required package: grid
Loading required package: colorspace
Loading required package: lattice

An object of class Biclust 

call:
	biclust(x = x, method = BCXmotifs(), ns = 20, nd = 20, sd = 5, 
	    alpha = 0.01, number = 10)

Number of Clusters found:  10 

First  5  Cluster sizes:
                   BC 1 BC 2 BC 3 BC 4 BC 5
Number of Rows:     203   86   51   12   10
Number of Columns:    6    6    6   14   11

biclust documentation built on May 2, 2019, 5:56 p.m.