testAnnot: Find samples annotations over-represented covariates in...

In BicARE: Biclustering Analysis and Results Exploration

Description

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

Usage

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

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

BicARE documentation built on Nov. 8, 2020, 7:47 p.m.