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Multiple Tests Correction Through Post-hoc Inference

Source: R/postHocTest.r
postHocTest.Rd

Wrapper function around sanssouci::posthocBySimes (Blanchard et al., 2020, doi:10.1214/19-AOS1847) for multiple tests correction through post-hoc inference.

Usage

postHocTest(SExp, predicate, alpha, tdpLowerBound, verbose = TRUE)

Arguments

SExp

An object that inherits from the SummarizedExperiment class and augmented with the results of the differential expression analysis.

predicate

A predicate function that returns a single TRUE or FALSE if the regions on which it is applied meets the conditions defined in the predicate. The criteria used in the predicate have to be defined for each regions in mcols(SExp).

alpha

A Double. The significance level of the (post-hoc) confidence bound on the type 1 error (See sanssouci::posthocBySimes).

tdpLowerBound

A value for the minimum true positive rate on the returned set of rejected regions.

verbose

A Logical. Should all the operations performed be displayed ?

Value

The SExp input object augmented with the metadata column DER. DER is set to TRUE if the region is called differentially expressed.