| 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) a 2x2 enrichment contingency table for its appropriate use in package goSorensen. It is internally used by function 'buildEnrichTable'.. |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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 |
| 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 terms 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' |
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