exploreOnlybic: The exploreOnlybic function
In BcDiag: Diagnostics Plots for Bicluster Data

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

Provides exploratory plots only for biclustering results.

1 2	exploreOnlybic(dset, bres, pfor= "all", gby= "genes", mname="biclust",bnum=1, fabia.thresZ=0.5,fabia.thresL=NULL)

`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).

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

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.

Mengsteab Aregay mycs.zab@gmail.com

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.

exploreBic

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)