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'))

Peer review:

Datasets:
  • BP.4 - An example of an object of class "equivSDhtestList" resulting from a call to 'equivSorensenTest'
  • allOncoGeneLists - 7 gene lists possibly related with cancer
  • 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'
  • cancerEquivSorensen - An example of an object of class "AllEquivSDhtest" resulting from a call to 'allEquivTestSorensen'
  • pbtGeneLists - 14 gene lists possibly related with kidney transplant rejection
  • tab_atlas.sanger_BP3 - Cross-tabulation of enriched GO terms at level 3 of ontology BP in two gene lists
  • waldman_atlas.BP.4 - An example of an object of class "equivSDhtest" resulting from a call to function 'equivSorensenTest'

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

4.52 score 11 scripts 177 downloads 22 exports 117 dependencies

Last updated 23 days agofrom:88ed3715d9. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winNOTENov 18 2024
R-4.5-linuxNOTENov 18 2024
R-4.4-winNOTENov 18 2024
R-4.4-macNOTENov 18 2024
R-4.3-winNOTENov 18 2024
R-4.3-macNOTENov 18 2024

Exports:allBuildEnrichTableallEquivTestSorensenallHclustThresholdallSorenThresholdbuildEnrichTabledSorensenduppSorensenenrichedInequivTestSorensengetDissimilaritygetEffNbootgetNbootgetPvaluegetSEgetTablegetUpperhclustThresholdnice2x2TablepruneClustsseSorensensorenThresholdupgrade

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

An Introduction to goSorensen R-Package

Jordi Ocaña, Pablo Flores

Rendered fromgoSorensen_Introduction.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2024-07-31
Started: 2022-06-16

An Irrelevance Threshold Matrix of Dissimilarities.

Pablo Flores, Jordi Ocaña

Rendered fromirrelevance-threshold_Matrix_Dissimilarities.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2024-07-30
Started: 2024-07-30

README

Rendered fromREADME.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2024-07-30
Started: 2024-07-30

Readme and manuals

Help Manual

Help pageTopics
Iterate 'buildEnrichTable' along the specified GO ontologies and GO levelsallBuildEnrichTable
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
An example of an object of class "allTableList" resulting from a call to 'buildEnrichTable'allTabs
An example of an object of class "tableList" resulting from a call to 'buildEnrichTable'allTabsBP.4
An example of object of class "AllEquivSDhtest" resulting from a call to 'allEquivTestSorensen'boot.cancerEquivSorensen
Studentized Sorensen-Dice dissimilarity statisticboot.tStat
An example of an object of class "equivSDhtestList" resulting from a call to 'equivSorensenTest'BP.4
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
An example of an object of class "AllEquivSDhtest" resulting from a call to 'allEquivTestSorensen'cancerEquivSorensen
Reformats and completes (if necessary) a 2x2 enrichment contingency table for its appropriate use in package goSorensen. It is internally used by function 'buildEnrichTable'..completeTable
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
Equivalence test based on the Sorensen-Dice dissimilarityequivTestSorensen equivTestSorensen.character equivTestSorensen.list equivTestSorensen.matrix equivTestSorensen.numeric equivTestSorensen.table equivTestSorensen.tableList
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
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
Cross-tabulation of enriched GO terms at level 3 of ontology BP in two gene liststab_atlas.sanger_BP3
Update the result of a Sorensen-Dice equivalence test.upgrade upgrade.AllEquivSDhtest upgrade.equivSDhtest upgrade.equivSDhtestList
An example of an object of class "equivSDhtest" resulting from a call to function 'equivSorensenTest'waldman_atlas.BP.4