Learn R Programming

BcDiag (version 1.0.10)

exploreOnlybic: The exploreOnlybic function

Description

Provides exploratory plots only for biclustering results.

Usage

exploreOnlybic(dset, bres, pfor= "all", gby= "genes", mname="biclust",bnum=1, fabia.thresZ=0.5,fabia.thresL=NULL)

Arguments

dset
data matrix.
bres
biclustering result.
gby
group bicluster; 'genes' or 'conditions'.
pfor
fit a plot for 'mean', 'median', 'variance', 'mad', 'all', or 'quant' (quantile).
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).

Value

Summary plot will display only for biclustered data.Note that the "biclust" option for mname will also accept results from the packages iBBiG and rqubic.

Details

The exploreOnlybic function has similar function with exploreBic. The only difference is that it provides exploratory plots only for biclustered data.

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.

Hochreiter, S., Bodenhofer, U., Heusel, M.et al. (2010).FABIA: factor analysis for bicluster acquisition. Bioinformatices, 26, 1520-1527.

See Also

exploreBic

Examples

Run this code
data(breastc)
# find bicluster using biclust algorithm
library(biclust)
bic <- biclust(breastc,method=BCPlaid())
# Plot the median of biclusterd data.
exploreOnlybic(dset=breastc, bres=bic, pfor="all", gby="genes", mname="biclust", bnum=1)

Run the code above in your browser using DataLab