# Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

## Documentation for package ‘goSorensen’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H N P S U

goSorensen-package | gosorensen: A package for making inference on gene lists based on the Sorensen-Dice dissimilarity

## -- A --

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
allEquivTestSorensen.allTableList | Iterate 'equivTestSorensen' along the specified GO ontologies and GO levels
allEquivTestSorensen.list | 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
allSorenThreshold.allTableList | Iterate 'sorenThreshold' along the specified GO ontologies and GO levels
allSorenThreshold.list | Iterate 'sorenThreshold' along the specified GO ontologies and GO levels

## -- B --

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.
buildEnrichTable.character | Creates a 2x2 enrichment contingency table from two gene lists, or all pairwise contingency tables for a "list" of gene lists.
buildEnrichTable.default | Creates a 2x2 enrichment contingency table from two gene lists, or all pairwise contingency tables for a "list" of gene lists.
buildEnrichTable.list | Creates a 2x2 enrichment contingency table from two gene lists, or all pairwise contingency tables for a "list" of gene lists.

## -- C --

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.

## -- D --

dissMatrx_BP4 | Example of the output produced by the function 'sorenThreshold'. It contains the dissimilarity matrix at GO level 4, for the ontology BP.
dSorensen | Computation of the Sorensen-Dice dissimilarity
dSorensen.character | Computation of the Sorensen-Dice dissimilarity
dSorensen.list | Computation of the Sorensen-Dice dissimilarity
dSorensen.matrix | Computation of the Sorensen-Dice dissimilarity
dSorensen.numeric | Computation of the Sorensen-Dice dissimilarity
dSorensen.table | Computation of the Sorensen-Dice dissimilarity
dSorensen.tableList | Computation of the Sorensen-Dice dissimilarity
duppSorensen | Upper limit of a one-sided confidence interval (0, dUpp] for the Sorensen-Dice dissimilarity
duppSorensen.character | Upper limit of a one-sided confidence interval (0, dUpp] for the Sorensen-Dice dissimilarity
duppSorensen.list | Upper limit of a one-sided confidence interval (0, dUpp] for the Sorensen-Dice dissimilarity
duppSorensen.matrix | Upper limit of a one-sided confidence interval (0, dUpp] for the Sorensen-Dice dissimilarity
duppSorensen.numeric | Upper limit of a one-sided confidence interval (0, dUpp] for the Sorensen-Dice dissimilarity
duppSorensen.table | Upper limit of a one-sided confidence interval (0, dUpp] for the Sorensen-Dice dissimilarity
duppSorensen.tableList | Upper limit of a one-sided confidence interval (0, dUpp] for the Sorensen-Dice dissimilarity

## -- E --

enrichedIn | This function builds a cross-tabulation of enriched (TRUE) and non-enriched (FALSE) GO terms vs. gene lists
enrichedIn.character | This function builds a cross-tabulation of enriched (TRUE) and non-enriched (FALSE) GO terms vs. gene lists
enrichedIn.default | This function builds a cross-tabulation of enriched (TRUE) and non-enriched (FALSE) GO terms vs. gene lists
enrichedIn.list | 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
equivTestSorensen.character | Equivalence test based on the Sorensen-Dice dissimilarity
equivTestSorensen.list | Equivalence test based on the Sorensen-Dice dissimilarity
equivTestSorensen.matrix | Equivalence test based on the Sorensen-Dice dissimilarity
equivTestSorensen.numeric | Equivalence test based on the Sorensen-Dice dissimilarity
equivTestSorensen.table | Equivalence test based on the Sorensen-Dice dissimilarity
equivTestSorensen.tableList | Equivalence test based on the Sorensen-Dice dissimilarity

## -- F --

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.

## -- G --

getDissimilarity | Access to the estimated Sorensen-Dice dissimilarity in one or more equivalence test results
getDissimilarity.AllEquivSDhtest | Access to the estimated Sorensen-Dice dissimilarity in one or more equivalence test results
getDissimilarity.equivSDhtest | Access to the estimated Sorensen-Dice dissimilarity in one or more equivalence test results
getDissimilarity.equivSDhtestList | 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)
getEffNboot.AllEquivSDhtest | Access to the number of effective bootstrap replicates in one or more equivalence test results (only for their bootstrap version)
getEffNboot.equivSDhtest | Access to the number of effective bootstrap replicates in one or more equivalence test results (only for their bootstrap version)
getEffNboot.equivSDhtestList | 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)
getNboot.AllEquivSDhtest | Access to the number of initially planned bootstrap replicates in one or more equivalence test results (only in their bootstrap version)
getNboot.equivSDhtest | Access to the number of initially planned bootstrap replicates in one or more equivalence test results (only in their bootstrap version)
getNboot.equivSDhtestList | 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
getPvalue.AllEquivSDhtest | Access to the p-value of one or more equivalence test results
getPvalue.equivSDhtest | Access to the p-value of one or more equivalence test results
getPvalue.equivSDhtestList | 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
getSE.AllEquivSDhtest | Access to the estimated standard error of the sample Sorensen-Dice dissimilarity in one or more equivalence test results
getSE.equivSDhtest | Access to the estimated standard error of the sample Sorensen-Dice dissimilarity in one or more equivalence test results
getSE.equivSDhtestList | 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
getTable.AllEquivSDhtest | Access to the contingency table of mutual enrichment of one or more equivalence test results
getTable.equivSDhtest | Access to the contingency table of mutual enrichment of one or more equivalence test results
getTable.equivSDhtestList | 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
getUpper.AllEquivSDhtest | Access to the upper limit of the one-sided confidence intervals for the Sorensen-Dice dissimilarity in one or more equivalence test results
getUpper.equivSDhtest | Access to the upper limit of the one-sided confidence intervals for the Sorensen-Dice dissimilarity in one or more equivalence test results
getUpper.equivSDhtestList | 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
gosorensen | gosorensen: A package for making inference on gene lists based on the Sorensen-Dice dissimilarity

## -- H --

hclustThreshold | From a Sorensen-Dice threshold dissimilarity matrix, generate an object of class "hclust"

## -- N --

nice2x2Table | Checks for validity data representing an enrichment contingency table generated from two gene lists
nice2x2Table.matrix | Checks for validity data representing an enrichment contingency table generated from two gene lists
nice2x2Table.numeric | Checks for validity data representing an enrichment contingency table generated from two gene lists
nice2x2Table.table | Checks for validity data representing an enrichment contingency table generated from two gene lists

## -- P --

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"

## -- S --

seSorensen | Standard error of the sample Sorensen-Dice dissimilarity, asymptotic approach
seSorensen.character | Standard error of the sample Sorensen-Dice dissimilarity, asymptotic approach
seSorensen.list | Standard error of the sample Sorensen-Dice dissimilarity, asymptotic approach
seSorensen.matrix | Standard error of the sample Sorensen-Dice dissimilarity, asymptotic approach
seSorensen.numeric | Standard error of the sample Sorensen-Dice dissimilarity, asymptotic approach
seSorensen.table | Standard error of the sample Sorensen-Dice dissimilarity, asymptotic approach
seSorensen.tableList | 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.
sorenThreshold.list | For a given level (2, 3, ...) in a GO ontology (BP, MF or CC), compute the equivalence threshold dissimilarity matrix.
sorenThreshold.tableList | For a given level (2, 3, ...) in a GO ontology (BP, MF or CC), compute the equivalence threshold dissimilarity matrix.

## -- U --

upgrade | Update the result of a Sorensen-Dice equivalence test.
upgrade.AllEquivSDhtest | Update the result of a Sorensen-Dice equivalence test.
upgrade.equivSDhtest | Update the result of a Sorensen-Dice equivalence test.
upgrade.equivSDhtestList | Update the result of a Sorensen-Dice equivalence test.