Package: methylclock 1.13.0
methylclock: Methylclock - DNA methylation-based clocks
This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath's clock, Hannum's clock, BNN, Horvath's skin+blood clock, PedBE clock and Wu's clock. Gestational DNAm age : Knight's clock, Bohlin's clock, Mayne's clock and Lee's clocks. Biological DNAm clocks : Levine's clock and Telomere Length's clock.
Authors:
methylclock_1.13.0.tar.gz
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methylclock.pdf |methylclock.html✨
methylclock/json (API)
NEWS
# Install 'methylclock' in R: |
install.packages('methylclock', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/isglobal-brge/methylclock/issues
- progress_data - PROGRESS cohor data
- progress_vars - PROGRESS cohort variables
On BioConductor:methylclock-1.13.0(bioc 3.21)methylclock-1.12.0(bioc 3.20)
dnamethylationbiologicalquestionpreprocessingstatisticalmethodnormalizationcpp
Last updated 2 months agofrom:5639edc30c. Checks:OK: 1 NOTE: 8. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 29 2024 |
R-4.5-win-x86_64 | NOTE | Nov 29 2024 |
R-4.5-linux-x86_64 | NOTE | Nov 29 2024 |
R-4.4-win-x86_64 | NOTE | Nov 29 2024 |
R-4.4-mac-x86_64 | NOTE | Nov 29 2024 |
R-4.4-mac-aarch64 | NOTE | Nov 29 2024 |
R-4.3-win-x86_64 | NOTE | Nov 29 2024 |
R-4.3-mac-x86_64 | NOTE | Nov 29 2024 |
R-4.3-mac-aarch64 | NOTE | Nov 29 2024 |
Exports:checkClockscheckClocksGAcommonClockCpgsDNAmAgeDNAmGAgetCellTypeReferenceload_DNAm_Clocks_dataload_DNAmGA_Clocks_datameffilEstimateCellCountsFromBetasmeffilListCellTypeReferencesplotCorClocksplotDNAmAge
Dependencies:abindannotateAnnotationDbiAnnotationForgeAnnotationHubAnnotationHubDataaskpassbackportsbase64base64encbeanplotBHBiobaseBiocBaseUtilsBiocCheckBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiocViewsbiomaRtBiostringsbitbit64bitopsblobbootbrewbriobroombslibbumphuntercachemcallrcarcarDatacellrangerclicliprclustercodetoolscolorspacecommonmarkconfintrconflictedcorrplotcowplotcpp11crayoncredentialscurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsDerivdescdevtoolsdiffobjdigestdoBydoRNGdownlitdplyrdtplyrdynamicTreeCutellipsisevaluateExperimentHubExperimentHubDatafansifarverfastmapfilelockfontawesomeforcatsforeachformatRFormulafsfutile.loggerfutile.optionsgarglegenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOquerygertggplot2ggpmiscggppggpubrggrepelggsciggsignifghgitcredsgluegoogledrivegooglesheets4graphgridExtragtablehavenHDF5Arrayhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2idsilluminaioimputeiniIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelifecyclelimmalme4lmodel2locfitlubridatemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmemoisemethylclockDatamgcvmicrobenchmarkmimeminfiminiUIminqamodelrmultcompmultcompViewmulttestmunsellmvtnormnlmenloptrnnetnor1mixnumDerivopensslOrganismDbipbkrtestPerformanceAnalyticspillarpkgbuildpkgconfigpkgdownpkgloadplanetplogrplyrpngpolynompraisepreprocessCoreprettyunitsprocessxprofvisprogresspromisespspurrrquadprogquantregR.methodsS3R.ooR.utilsR6raggrappdirsRBGLrcmdcheckRColorBrewerRcppRcppEigenRCurlreadrreadxlrematchrematch2remotesrentrezreprexreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrngtoolsroxygen2RPMMrprojrootRsamtoolsRSQLiterstatixrstudioapirtracklayerRUnitrversionsrvestS4ArraysS4VectorssandwichsassscalesscrimeselectrsessioninfoshinysiggenessnowsourcetoolsSparseArraySparseMsparseMatrixStatssplus2RstatmodstringdiststringistringrSummarizedExperimentsurvivalsyssystemfontstestthattextshapingTH.datatibbletidyrtidyselecttidyversetimechangetinytextxdbmakertzdbUCSC.utilsurlcheckerusethisutf8uuidvctrsviridisLitevroomwaldowhiskerwithrxfunXMLxml2xopenxtablextsXVectoryamlzipzlibbioczoo
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Check wheter input data contains the required CpGs for the implemented clocks. | checkClocks |
Check wheter input data contains the required CpGs for the implemented clocks for Gestational Age. | checkClocksGA |
Get common CpGs | commonClockCpgs |
DNAm age estimation using different DNA methylation clocks. | DNAmAge |
Gestational DNAm age estimation using different DNA methylation clocks. | DNAmGA |
Get cell type reference | getCellTypeReference |
Loads DNAm clock data from methylclockData | load_DNAm_Clocks_data |
Loads DNAmGA clock data from methylclockData | load_DNAmGA_Clocks_data |
Estimate cell counts for a beta matrix from a reference | meffilEstimateCellCountsFromBetas |
List of available cell type references | meffilListCellTypeReferences |
methylclock | methylclock |
Plot correlation among DNAm clockx | plotCorClocks |
Plot DNAm age estimation vs chronological age. | plotDNAmAge |
PROGRESS cohor data | progress_data |
PROGRESS cohort variables | progress_vars |