Find samples annotations over-represented covariates in biclusters

Share:

Description

Characterisation of the biclusters in term of over-representation of sample covariates.

Usage

1
testAnnot(resBic, annot=NULL, covariates="all")

Arguments

resBic

a biclustering result from FLOC

annot

annotation matrix, default value is set to NULL, then phenoData of the ExpressionSet is used

covariates

the names of the covariates that should be tested, default value is set to "all"

Details

For each bicluster and each covariate a chi-squarred test is performed to test the adequation between the distribution of the levels of the covariates in the bicluster and in the original dataset.

Multiple testing correction is performed by the Benjamini-Yekutieli procedure. The residuals of the tests indicate if the level is over or down represented in the bicluster.

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

Value

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

The results are presented as a list with :

covar

the samples covariates tested

pvalues

a matrix with the p-values of the tests

adjpvalues

a matrix with the p-values adjusted by the Benjamini Yekutieli procedure

index

a list of matrices with the numbers of each level in each bicluster

residuals

a list of matrices with the residuals of the tests for each modality in each bicluster

Author(s)

Pierre Gestraud

Examples

1
2
data(sample.biclustering)
resBic <- testAnnot(sample.biclustering, annot=NULL, covariates=c("sex", "type"))