anomedOnlybic {BcDiag}

R Documentation

The anomedOnlybic function

Description

Provides ANOVA and median polish residual plots for biclustered data.

Usage

anomedOnlybic(dset, bres, fit="boxplot", mname="biclust", bnum=1, 
fabia.thresZ=0.5,fabia.thresL=NULL)

Arguments

dset	data matrix.
bres	bicluster result.
fit	a string value to fit a plot; 'aplot','mplot','anovbplot','mpolishbplot','boxplot'.
mname	method name; 'biclust', 'isa2', 'fabia' or 'bicare'.
bnum	existing biclusters; '1','2'...
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

A function provides residuals plots for biclustered data based on ANOVA and median polish.

The function checks the required parameter values and fit the plot according to the user requirements.

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

Value

Residual plots or residual box plots.

Author(s)

Mengsteab Aregay mycs.zab@gmail.com

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.

Examples

data(breastc)
library(biclust)
# find bicluster using one of biclust algorithms

bic <- biclust(breastc, method=BCPlaid())
# fit residual boxplot from ANOVA
anomedOnlybic(dset=breastc,bres=bic,fit="boxplot",mname="biclust")

---