Description Usage Arguments Details Value Author(s) References See Also Examples
This function compares several clustering methods (link functions and distances) by means of its stability.
1 2 3 4 |
X |
a data frame with p rows and n columns; if clustering on genes - samples by row and genes by column; if clustering on samples genes by row and samples by column |
nb |
number of classes for partition; it must start at 2 and be sequential(by default 2,3 and 4) |
f |
part of the data set which is randomly picked for each subsample in the resampling procedure (by default 0.8) |
nsub |
half of the number of times the perturbation procedure is applied in the resampling procedure (by default 100) |
list_DIS |
the list of distances to test |
list_ALGO |
the list of linkage method to test |
s0 |
similarity threshold, must lie between 0 and 1 (by default 0.98) |
pdfname |
pdf file name for saving graphic, by default = NULL |
verbose |
print results if verbose = TRUE, by default = TRUE |
Resampling is done by randomly picking without replacement f of the data set; similarity threshold is the value which is pertinent to decide that two partitions are similar; see references
stab.methods |
a list containing methods declared stable for each partition |
Returns a graphic containing the frequencies of methods declared stable
Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupe
http://bioinfo-out.curie.fr/projects/cgh-clustering/index.html
1 2 3 4 5 6 7 | data(marty)
## Test on a smaller dataset
## Not run:
example.data<-marty[1:100,]
stab<-eval.stability.clustering(example.data)
## End(Not run)
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