BcDiag (version 1.0.2)

writeBic: The writeBic function

Description

Provides a summary output in a text format, extracted from 'biclust','isa2' and 'fabia' bicluster algorithms.

Usage

writeBic(dset, fileName, bicResult, bicname, 
mname = c("fabia", "isa2", "biclust"), append = TRUE, delimiter = " ")

Arguments

dset

Data matrix

fileName

The name of the bicluster file to be saved.

bicResult

bicluster result obtained from 'biclust','isa2' or 'fabia'

bicname

the tilte to be given for the biclusterd data.

mname

method name; 'biclust', 'isa2' or 'fabia'

append

logical value; 'true' or 'false

delimiter

default value is " ".

Value

• Biclusterd text file with title, total number of biclusterd, dimention and name of the biclusterd genes(rows) or conditions(columns).

Details

The original function was developed in 'biclust' package by Kaiser et.al (2008). we extend the function to be used for further bicluster algorithms, such as; 'isa2' and 'fabia'.

References

Van't Veer, L.J., Dai, H., van de Vijver, M.J., He, Y.D., Hart, A.A. et al. (2002). Gene expression profiling predicts clinical outcome of breast cancer,Nature, 415, 530-536. Kaiser S. and Leisch F. (2008). A Toolbox for Bicluster Analysis in R. Ludwigstrasse. 33. Csardi G., Kutalik Z., and Bergmann S.(2010). Modular analysis of gene expression data with R. Bioinformatics, 26, 1376-7

See Also

biclust

Examples

#manupilate the biclust result
data(breastc)
fab<- fabia(breastc)
#write the bicluster result in to a text
writeBic(dset=breastc,fileName="fabiabreast.txt",
bicResult=fab, bicname="Biclust results for fabia",
mname="fabia")