ensemble {biclust} | R Documentation |
Calculates an ensemble of biclusters from different parameter setting of possible different bicluster algorithms.
ensemble(x, confs, rep = 1, maxNum = 5, similar = jaccard2, thr = 0.8, simthr =0.7, subs = c(1, 1), bootstrap = FALSE, support = 0, combine=firstcome, ...)
x |
Data Matrix |
confs |
Matrix containing parameter sets |
rep |
Number of repetitions for each parameter set |
maxNum |
Maximum number of biclusters taken from each run |
similar |
Function to produce a similarity matrix of bicluster |
thr |
Threshold for similarity |
simthr |
Proportion of row column combinations in bicluster |
subs |
Vector of proportion of rows and columns for subsampling. Default c(1,1) means no subsampling. |
bootstrap |
Should bootstrap sampling be used (logical: replace=bootstrap). |
support |
Which proportion of the runs must contain the bicluster to have enough support to report it (between 0 and 1). |
combine |
Function to combine the single bicluster only firstcome and hcl for hierarchical clustering are possible at the moment. |
... |
Arguments past to the combine function. |
Two different kinds (or both combined) of ensembling is possible. Ensemble of repeated runs or ensemble of runs on subsamples.
Return an object of class Biclust
Sebastian Kaiser sebastian.kaiser@stat.uni-muenchen.de
Biclust-class
, plaid.grid
, bimax.grid
## Not run: data(BicatYeast) ensemble.plaid <- ensemble(BicatYeast,plaid.grid()[1:5],rep=1,maxNum=2, thr=0.5, subs = c(1,1)) ensemble.plaid x <- binarize(BicatYeast) ensemble.bimax <- ensemble(x,bimax.grid(),rep=10,maxNum=2,thr=0.5, subs = c(0.8,0.8)) ensemble.bimax ## End(Not run)