R: The Xmotifs Bicluster algorithm

BCXmotifs {biclust} | R Documentation

## 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 sebastian.kaiser@stat.uni-muenchen.de

### 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

[Package biclust version 2.0.2 Index]