exploreOnlybic {BcDiag}

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).

Details

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

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.

Author(s)

Mengsteab Aregay [e-mail]

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

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)