BCXmotifs {biclust}

The Xmotifs Bicluster algorithm

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