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

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Documentation for package ‘goSorensen’ version 1.10.0

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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.