testSet: Find gene sets that are enriched in a bicluster
In BicARE: Biclustering Analysis and Results Exploration

Description Usage Arguments Details Value Author(s) Examples

View source: R/testSet.R

Test of the over-representation of gene sets in the biclusters

1	testSet(resBic, geneSetCol)

`resBic`	a `biclustering` object created by `FLOC`
`geneSetCol`	a `GeneSetCollection-class`

The over-representation of a gene set in a bicluster is evaluated by an hypergeometric test.

The genes identifiers of the gene sets will automatically be mapped to the same as those used in the data.

Due to the amount of results it is advised to use the makeReport function to get a html report.

A biclustering object containing resBic and updated with the results of the tests in resBic$geneSet.

The results are presented as a list with :

`GeneSetCollection`	the GeneSetCollection used
`pvalues`	a matrix containing the pvalues of the tests for each geneSet and each bicluster
`adjpvalue`	a matrix containing the p-values adjusted by the Benjamini Yekutieli procedure

Pierre Gestraud pierre.gestraud@curie.fr

1
2
3

data(sample.biclustering)
gss <- GeneSetCollection(sample.biclustering$ExpressionSet[1:50,], setType=GOCollection())
resBic <- testSet(sample.biclustering, gss)