stdTest4GOIDs: StandardTest4GOIDs

In ASPresearch/equivStandardTest: Implements a standard test of equivalence as described in (Sanchez et alt. 2019)

StandardTest4GOIDs

Description

This function performs a "standard test" of equivalence between two lists of enriched GOTerms The lists are intended to have been obtained from enrichment analyses performed on two gene lists Given that this version of the test does not provide gene lists only "unrestricted" crosstabulation can be performed That is, all terms in the given GO level are used to build the table, even if they are not found in the geneLists's annotations.

Usage

stdTest4GOIDs(GO1, GO2, onto, GOLevel, listNames = NULL)

Arguments

GO1	character vector containing a FIRST list of GO identifiers
GO2	character vector containing a SECOND gene list GO identifiers
onto	string describing the ontology. Belongs to c('BP', 'MF', 'CC', 'ANY')
listNames	character vector with names of the genelists that generated the enriched GOIDs
GOLev	An integer

Examples

 GOIDs2 <-kidneyEnrichedGOIDs[[2]]
 data(kidneyEnrichedGOIDs)
 GOIDs1 <-kidneyEnrichedGOIDs[[1]]
 names4lists<- names(kidneyEnrichedGOIDs)[1:2]
 anOnto <- 'BP'
 GOLev<- 3
 testedFromGOIds <- stdTest4GOIDs (GO1 = GOIDs1, GO2 = GOIDs2, onto = anOnto, 
 GOLevel =GOLev, listNames=names4lists)

ASPresearch/equivStandardTest documentation built on March 28, 2022, 4:31 p.m.