BcDiag (version 1.0.4)

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 title to be given for the biclustered data.

mname

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

append

logical value; TRUE as default

delimiter

delimiter in created output file; default value is " ".

Value

• Biclustered text file with title, total number of biclustered, dimension and name of the biclustered 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

# create the biclustering result
data(breastc)
library(fabia)
fab<- fabia(breastc)
# write the biclustering result into a text file
writeBic(dset=breastc,fileName="fabiabreast.txt",
bicResult=fab, bicname="Biclust results for fabia",
mname="fabia")