allBuildEnrichTable     Iterate 'buildEnrichTable' along the specified
                        GO ontologies and GO levels
allContTabs             Example of the output produced by the function
                        'allBuildEnrichTable'.
allDissMatrx            Example of the output produced by the function
                        'allSorenThreshold'. It contains the
                        dissimilarity matrices for GO levels from 3 to
                        10 across the ontologies BP, CC and MF.
allEqTests              Example of the output produced by the function
                        'allEquivTestSorensen' using the normal
                        asymptotic distribution.
allEqTests_boot         Example of the output produced by the function
                        'allEquivTestSorensen' using the approximated
                        bootstrap distribution.
allEquivTestSorensen    Iterate 'equivTestSorensen' along the specified
                        GO ontologies and GO levels
allHclustThreshold      Iterate 'hclustThreshold' along the specified
                        GO ontologies and GO levels
allOncoGeneLists        7 gene lists possibly related with cancer
allSorenThreshold       Iterate 'sorenThreshold' along the specified GO
                        ontologies and GO levels
boot.tStat              Studentized Sorensen-Dice dissimilarity
                        statistic
buildEnrichTable        Creates a 2x2 enrichment contingency table from
                        two gene lists, or all pairwise contingency
                        tables for a "list" of gene lists.
cont_all_BP4            Example of the output produced by the function
                        'buildEnrichTable'. It contains the enrichment
                        contingency tables for all the lists from
                        'allOncoGeneLists' at level 4 of ontology BP.
cont_atlas.sanger_BP4   Example of the output produced by the function
                        'buildEnrichTable'. It contains the enrichment
                        contingency table for two lists at level 4 of
                        ontology BP.
dSorensen               Computation of the Sorensen-Dice dissimilarity
dissMatrx_BP4           Example of the output produced by the function
                        'sorenThreshold'. It contains the dissimilarity
                        matrix at GO level 4, for the ontology BP.
duppSorensen            Upper limit of a one-sided confidence interval
                        (0, dUpp] for the Sorensen-Dice dissimilarity
enrichedIn              This function builds a cross-tabulation of
                        enriched (TRUE) and non-enriched (FALSE) GO
                        terms vs. gene lists
enrichedInBP4           Example of the output produced by the function
                        'enrichedIn'. It contains exclusively GO terms
                        enriched in at least one list of
                        'allOncoGeneLists', ontology BP, GO-Level 4.
eqTest_all_BP4          Example of the output produced by the function
                        'equivTestSorensen'. It contains all the
                        possible equivalence tests for the lists from
                        'allOncoGeneLists' at level 4 of ontology BP.
eqTest_atlas.sanger_BP4
                        Example of the output produced by the function
                        'equivTestSorensen'. It contains the
                        equivalence test for comparing two lists at
                        level 4 of ontology BP.
equivTestSorensen       Equivalence test based on the Sorensen-Dice
                        dissimilarity
fullEnrichedInBP4       Example of the output produced by the function
                        'enrichedIn'. It contains all the GO terms
                        enriched or not-enriched in the lists of
                        'allOncoGeneLists', ontology BP, GO-Level 4.
getDissimilarity        Access to the estimated Sorensen-Dice
                        dissimilarity in one or more equivalence test
                        results
getEffNboot             Access to the number of effective bootstrap
                        replicates in one or more equivalence test
                        results (only for their bootstrap version)
getNboot                Access to the number of initially planned
                        bootstrap replicates in one or more equivalence
                        test results (only in their bootstrap version)
getPvalue               Access to the p-value of one or more
                        equivalence test results
getSE                   Access to the estimated standard error of the
                        sample Sorensen-Dice dissimilarity in one or
                        more equivalence test results
getTable                Access to the contingency table of mutual
                        enrichment of one or more equivalence test
                        results
getUpper                Access to the upper limit of the one-sided
                        confidence intervals for the Sorensen-Dice
                        dissimilarity in one or more equivalence test
                        results
gosorensen              gosorensen: A package for making inference on
                        gene lists based on the Sorensen-Dice
                        dissimilarity
hclustThreshold         From a Sorensen-Dice threshold dissimilarity
                        matrix, generate an object of class "hclust"
nice2x2Table            Checks for validity data representing an
                        enrichment contingency table generated from two
                        gene lists
pbtGeneLists            14 gene lists possibly related with kidney
                        transplant rejection
pruneClusts             Remove all NULL or unrepresentable as a
                        dendrogram "equivClustSorensen" elements in an
                        object of class "equivClustSorensenList"
seSorensen              Standard error of the sample Sorensen-Dice
                        dissimilarity, asymptotic approach
sorenThreshold          For a given level (2, 3, ...) in a GO ontology
                        (BP, MF or CC), compute the equivalence
                        threshold dissimilarity matrix.
upgrade                 Update the result of a Sorensen-Dice
                        equivalence test.
