Description of implemented clocks | Chronological DNAm age (in years) | Gestational DNAm age (in weeks) | Getting started | DNA Methylation clocks | Data format | Data nomalization | Missing individual's data | Missing CpGs of DNAm clocks | Cell counts | Chronological and biological DNAm age estimation | Data in Horvath's format (e.g. csv with CpGs in rows) | Age acceleration | Chronological age prediction using ExpressionSet data | Use of DNAmAge in association studies | Use of DNAm age in children | Gestational DNAm age estimation | Model predicion | Correlation among DNAm clocks | References
Package: methylclock 1.19.0
Dolors Pelegri-Siso
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_1.19.0.tar.gz
methylclock_1.19.0.zip(r-4.7)methylclock_1.19.0.zip(r-4.6)methylclock_1.19.0.zip(r-4.5)
methylclock_1.19.0.tgz(r-4.6-x86_64)methylclock_1.19.0.tgz(r-4.6-arm64)methylclock_1.19.0.tgz(r-4.5-x86_64)methylclock_1.19.0.tgz(r-4.5-arm64)
methylclock_1.19.0.tar.gz(r-4.7-arm64)methylclock_1.19.0.tar.gz(r-4.7-x86_64)methylclock_1.19.0.tar.gz(r-4.6-arm64)methylclock_1.19.0.tar.gz(r-4.6-x86_64)
methylclock_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
methylclock/json (API)
| # 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
Datasets:
- progress_data - PROGRESS cohor data
- progress_vars - PROGRESS cohort variables
On BioConductor:methylclock-1.19.0(bioc 3.24)methylclock-1.18.0(bioc 3.23)
dnamethylationbiologicalquestionpreprocessingstatisticalmethodnormalizationcpp
Last updated from:0fec6e84d9. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 304 | ||
| linux-devel-arm64 | NOTE | 642 | ||
| linux-devel-x86_64 | NOTE | 685 | ||
| source / vignettes | OK | 686 | ||
| linux-release-arm64 | NOTE | 581 | ||
| linux-release-x86_64 | NOTE | 705 | ||
| macos-release-arm64 | NOTE | 430 | ||
| macos-release-x86_64 | NOTE | 837 | ||
| macos-oldrel-arm64 | NOTE | 482 | ||
| macos-oldrel-x86_64 | NOTE | 949 | ||
| windows-devel | NOTE | 797 | ||
| windows-release | NOTE | 914 | ||
| windows-oldrel | NOTE | 871 | ||
| wasm-release | OK | 270 |
Exports:checkClockscheckClocksGAcommonClockCpgsDNAmAgeDNAmGAgetCellTypeReferenceload_DNAm_Clocks_dataload_DNAmGA_Clocks_datameffilEstimateCellCountsFromBetasmeffilListCellTypeReferencesplotCorClocksplotDNAmAge
Dependencies:abindannotateAnnotationDbiAnnotationForgeAnnotationHubAnnotationHubDataaskpassbackportsbase64base64encbeanplotBHBiobaseBiocBaseUtilsBiocCheckBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiocVersionbiocViewsBiostringsbitbit64bitopsblobbootbrewbriobroombslibbumphuntercachemcallrcarcarDatacaToolscellrangercigarilloclicliprclustercodetoolscolorspacecommonmarkconfintrconflictedcorrplotcowplotcpp11crayoncredentialscurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsDerivdescdevtoolsdiffobjdigestdir.expirydoBydoRNGdownlitdplyrdtplyrdynamicTreeCutellipsisevaluateExperimentHubExperimentHubDatafansifarverfastmapfilelockfontawesomeforcatsforeachforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgarglegenefiltergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGEOquerygertggplot2ggpmiscggppggpubrggrepelggsciggsignifgitcredsgluegoogledrivegooglesheets4graphgridExtragtableh5mreadhavenHDF5Arrayhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2idsilluminaioimputeiniIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelifecyclelimmalme4lmtestlocfitlubridatemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmemoisemethylclockDatamgcvmicrobenchmarkmimeminfiminiUIminqamodelrmulttestnlmenloptrnnetnor1mixnumDerivopensslOrganismDbiotelpakpbkrtestPerformanceAnalyticspillarpkgbuildpkgconfigpkgdownpkgloadplanetplyrpngpolynompraisepreprocessCoreprettyunitsprocessxprofvisprogresspromisespspurrrquadprogquantregR.methodsS3R.ooR.utilsR6raggrappdirsRBGLrbibutilsrcmdcheckRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreadrreadxlreformulasrematchrematch2rentrezreprexreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrngtoolsroxygen2RPMMrprojrootRsamtoolsRSQLiterstatixrstudioapirtracklayerRUnitrversionsrvestS4ArraysS4VectorsS7sassscalesscrimeselectrSeqinfosessioninfoshinysiggenessnowsourcetoolsSparseArraySparseMsparseMatrixStatssplus2RstatmodstringdiststringistringrSummarizedExperimentsurvivalsyssystemfontstestthattextshapingtibbletidyrtidyselecttidyversetimechangetimeDatetinytextzdbUCSC.utilsurcaurlcheckerusethisutf8uuidvctrsviridisLitevroomwaldowhiskerwithrxfunXMLxml2xopenxtablextsXVectoryamlzipzoo
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 |
