BcDiag (version 1.0.2)

exploreBic: The exploreBic function

Description

Provides exploratory plots for biclusterd and. clusterd data parallely.

Usage

exploreBic(dset, bres, gby ="genes", pfor ="mean", mname ="biclust", bnum =1)

Arguments

dset

Data matrix.

bres

Bicluster result.

gby

group bicluster; 'genes' or 'conditions'.

pfor

plot for 'mean', 'median', 'variance', 'mad', 'all', or 'quantile'.

mname

Method name; 'biclust', 'isa2' or 'fabia'

bnum

Existed biclusters; '1','2'...

Value

• Summary plot will display according to the user specification.

Details

The exploreBic function is mainly used for exploratory data analysis. It provides summary plots for 'mean' 'median', 'variance', 'mad' and 'quantile plot'. The exploreBicfunction checked if the parameters are appropriately submitted and then it calls the indexedBicfunction to identify the biclust sub matrix and forwarded it to exploreCalc to be calculated its summary statistics. Finally, explorePlot will be invoked to display the required plot.

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

exploreOnlybic

Examples

data(breastc)
# find bicluster using biclust package
bic<- biclust(breastc,method=BCPlaid())
# Plot the mean of biclusterd and clustered genes parallely.
exploreBic(dset=breastc,bres=bic,gby="conditions",pfor="mean",mname="biclust")