Package: goSorensen 1.9.0

Pablo Flores

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

This package implements inferential methods to compare gene lists in terms of their biological meaning as expressed in the GO. The compared gene lists are characterized by cross-tabulation frequency tables of enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index. The fundamental guiding principle is that two gene lists are taken as similar if they share a great proportion of common enriched GO items.

Authors:Pablo Flores [aut, cre], Jordi Ocana [aut, ctb], Alexandre Sanchez-Pla [ctb], Miquel Salicru [ctb]

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goSorensen.pdf |goSorensen.html✨
goSorensen/json (API)
NEWS

# Install 'goSorensen' in R:
install.packages('goSorensen', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • 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.
  • allOncoGeneLists - 7 gene lists possibly related with cancer
  • 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.
  • dissMatrx_BP4 - Example of the output produced by the function 'sorenThreshold'. It contains the dissimilarity matrix at GO level 4, for the ontology BP.
  • 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.
  • 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.
  • pbtGeneLists - 14 gene lists possibly related with kidney transplant rejection

On BioConductor:goSorensen-1.9.0(bioc 3.21)goSorensen-1.8.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

annotationgogenesetenrichmentsoftwaremicroarraypathwaysgeneexpressionmultiplecomparisongraphandnetworkreactomeclusteringkegg

4.38 score 12 scripts 202 downloads 22 exports 116 dependencies

Last updated 9 days agofrom:a5e228c6ec. Checks:7 OK, 2 FAILURE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 19 2025
R-4.5-winOKMar 19 2025
R-4.5-macOKMar 19 2025
R-4.5-linuxOKMar 19 2025
R-4.4-winOKMar 19 2025
R-4.4-macOKMar 19 2025
R-4.4-linuxOKMar 19 2025
R-4.3-winOUTDATEDMar 18 2025
R-4.3-macOUTDATEDMar 18 2025

Exports:allBuildEnrichTableallEquivTestSorensenallHclustThresholdallSorenThresholdbuildEnrichTabledSorensenduppSorensenenrichedInequivTestSorensengetDissimilaritygetEffNbootgetNbootgetPvaluegetSEgetTablegetUpperhclustThresholdnice2x2TablepruneClustsseSorensensorenThresholdupgrade

Dependencies:AnnotationDbiapeaplotaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemcliclusterProfilercodetoolscolorspaceCompQuadFormcowplotcpp11crayoncurldata.tableDBIdigestDOSEdplyrenrichplotfansifarverfastmapfastmatchfgseaformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbgoProfilesGOSemSimgridGraphicsgsongtablehttrigraphIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslorg.Hs.eg.dbpatchworkpillarpkgconfigplogrplyrpngpolyclippurrrqvalueR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenreshape2rlangRSQLiteS4VectorsscalesscatterpiesnowstringistringrsyssystemfontstibbletidyrtidyselecttidytreetreeiotweenrUCSC.utilsutf8vctrsviridisLitewithrXVectoryulab.utils

An Introduction to goSorensen R-Package

Jordi Ocaña, Pablo Flores

Rendered fromgoSorensen_Introduction.Rmdusingknitr::rmarkdownon Mar 19 2025.

Last update: 2025-03-18
Started: 2022-06-16

Working with the Irrelevance-threshold Matrix of Dissimilarities.

Pablo Flores, Jordi Ocaña

Rendered fromDissimilarities_Matrix.Rmdusingknitr::rmarkdownon Mar 19 2025.

Last update: 2025-03-18
Started: 2025-03-18

Readme and manuals

Help Manual

Help pageTopics
Iterate 'buildEnrichTable' along the specified GO ontologies and GO levelsallBuildEnrichTable
Example of the output produced by the function 'allBuildEnrichTable'.allContTabs
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.allDissMatrx
Example of the output produced by the function 'allEquivTestSorensen' using the normal asymptotic distribution.allEqTests
Example of the output produced by the function 'allEquivTestSorensen' using the approximated bootstrap distribution.allEqTests_boot
Iterate 'equivTestSorensen' along the specified GO ontologies and GO levelsallEquivTestSorensen allEquivTestSorensen.allTableList allEquivTestSorensen.list
Iterate 'hclustThreshold' along the specified GO ontologies and GO levelsallHclustThreshold
7 gene lists possibly related with cancerallOncoGeneLists
Iterate 'sorenThreshold' along the specified GO ontologies and GO levelsallSorenThreshold allSorenThreshold.allTableList allSorenThreshold.list
Studentized Sorensen-Dice dissimilarity statisticboot.tStat
Creates a 2x2 enrichment contingency table from two gene lists, or all pairwise contingency tables for a "list" of gene lists.buildEnrichTable buildEnrichTable.character buildEnrichTable.default buildEnrichTable.list
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_all_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.cont_atlas.sanger_BP4
Example of the output produced by the function 'sorenThreshold'. It contains the dissimilarity matrix at GO level 4, for the ontology BP.dissMatrx_BP4
Computation of the Sorensen-Dice dissimilaritydSorensen dSorensen.character dSorensen.list dSorensen.matrix dSorensen.numeric dSorensen.table dSorensen.tableList
Upper limit of a one-sided confidence interval (0, dUpp] for the Sorensen-Dice dissimilarityduppSorensen duppSorensen.character duppSorensen.list duppSorensen.matrix duppSorensen.numeric duppSorensen.table duppSorensen.tableList
This function builds a cross-tabulation of enriched (TRUE) and non-enriched (FALSE) GO terms vs. gene listsenrichedIn enrichedIn.character enrichedIn.default enrichedIn.list
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.enrichedInBP4
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_all_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.eqTest_atlas.sanger_BP4
Equivalence test based on the Sorensen-Dice dissimilarityequivTestSorensen equivTestSorensen.character equivTestSorensen.list equivTestSorensen.matrix equivTestSorensen.numeric equivTestSorensen.table equivTestSorensen.tableList
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.fullEnrichedInBP4
Access to the estimated Sorensen-Dice dissimilarity in one or more equivalence test resultsgetDissimilarity getDissimilarity.AllEquivSDhtest getDissimilarity.equivSDhtest getDissimilarity.equivSDhtestList
Access to the number of effective bootstrap replicates in one or more equivalence test results (only for their bootstrap version)getEffNboot getEffNboot.AllEquivSDhtest getEffNboot.equivSDhtest getEffNboot.equivSDhtestList
Access to the number of initially planned bootstrap replicates in one or more equivalence test results (only in their bootstrap version)getNboot getNboot.AllEquivSDhtest getNboot.equivSDhtest getNboot.equivSDhtestList
Access to the p-value of one or more equivalence test resultsgetPvalue getPvalue.AllEquivSDhtest getPvalue.equivSDhtest getPvalue.equivSDhtestList
Access to the estimated standard error of the sample Sorensen-Dice dissimilarity in one or more equivalence test resultsgetSE getSE.AllEquivSDhtest getSE.equivSDhtest getSE.equivSDhtestList
Access to the contingency table of mutual enrichment of one or more equivalence test resultsgetTable getTable.AllEquivSDhtest getTable.equivSDhtest getTable.equivSDhtestList
Access to the upper limit of the one-sided confidence intervals for the Sorensen-Dice dissimilarity in one or more equivalence test resultsgetUpper getUpper.AllEquivSDhtest getUpper.equivSDhtest getUpper.equivSDhtestList
gosorensen: A package for making inference on gene lists based on the Sorensen-Dice dissimilaritygoSorensen-package goSorensen gosorensen
From a Sorensen-Dice threshold dissimilarity matrix, generate an object of class "hclust"hclustThreshold
Checks for validity data representing an enrichment contingency table generated from two gene listsnice2x2Table nice2x2Table.matrix nice2x2Table.numeric nice2x2Table.table
14 gene lists possibly related with kidney transplant rejectionpbtGeneLists
Remove all NULL or unrepresentable as a dendrogram "equivClustSorensen" elements in an object of class "equivClustSorensenList"pruneClusts
Standard error of the sample Sorensen-Dice dissimilarity, asymptotic approachseSorensen seSorensen.character seSorensen.list seSorensen.matrix seSorensen.numeric seSorensen.table seSorensen.tableList
For a given level (2, 3, ...) in a GO ontology (BP, MF or CC), compute the equivalence threshold dissimilarity matrix.sorenThreshold sorenThreshold.list sorenThreshold.tableList
Update the result of a Sorensen-Dice equivalence test.upgrade upgrade.AllEquivSDhtest upgrade.equivSDhtest upgrade.equivSDhtestList