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BcDiag (version 1.0.10)

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","bicare"), append = TRUE, delimiter = " ", fabia.thresZ=0.5,fabia.thresL=NULL)

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', 'fabia' or 'bicare'
append
logical value; TRUE as default
delimiter
delimiter in created output file; default value is " ".
fabia.thresZ
Bicluster threshold for mname="fabia". Threshold for sample belonging to bicluster; default 0.5.
fabia.thresL
Bicluster threshold for mname="fabia". Threshold for loading belonging to bicluster (if not given it is estimated).

Value

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', 'fabia' and 'bicare'.

Note that the "biclust" option for mname will also accept results from the packages iBBiG and rqubic.

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

Run this code
# 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")

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