writeBic: The writeBic function

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/writeBic.R

Description

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

Usage

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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).

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.

Value

Biclustered text file with title, total number of biclustered, dimension and name of the biclustered genes(rows) or conditions(columns).

Author(s)

Mengsteab Aregay

[email protected]

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

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# 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")

BcDiag documentation built on May 29, 2017, 6:17 p.m.