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

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Documentation for package ‘goSorensen’ version 1.4.0

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allBuildEnrichTable Iterate 'buildEnrichTable' along the specified GO ontologies and GO levels
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
allTabs An example of an object of class "allTableList" resulting from a call to 'buildEnrichTable'
allTabsBP.4 An example of an object of class "tableList" resulting from a call to 'buildEnrichTable'
boot.cancerEquivSorensen An example of object of class "AllEquivSDhtest" resulting from a call to 'allEquivTestSorensen'
boot.tStat Studentized Sorensen-Dice dissimilarity statistic
BP.4 An example of an object of class "equivSDhtestList" resulting from a call to 'equivSorensenTest'
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.
cancerEquivSorensen An example of an object of class "AllEquivSDhtest" resulting from a call to 'allEquivTestSorensen'
completeTable Reformats and completes (if necessary) an enrichment contingency table as is generated by function 'crossTabGOIDs4GeneLists', in order to make it appropriate for its use in package goSorensen.
crossTabGOIDs crossTabGOIDs
crossTabGOIDs4GeneLists crossTab4GeneLists
crossTabGOIDsUnrestricted crossTabGOIDsUnrestricted
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
enrichOnto enrichOnto
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
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
GOIDsInLevel GOIDsInLevel
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"
humanEntrezIDs Entrez Identifiers for all human genes contained in the org.Hs.eg.db package.
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
pbtGeneLists 5 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
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.
tab_atlas.sanger_BP3 Cross-tabulation of enriched GO items at level 3 of ontology BP in two gene lists
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.
waldman_atlas.BP.4 An example of an object of class "equivSDhtest" resulting from a call to function 'equivSorensenTest'