Package: methylclock 1.11.0

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:Dolors Pelegri-Siso [aut, cre], Juan R. Gonzalez [aut]

methylclock_1.11.0.tar.gz
methylclock_1.11.0.zip(r-4.5)methylclock_1.11.0.zip(r-4.4)methylclock_1.11.0.zip(r-4.3)
methylclock_1.11.0.tgz(r-4.4-arm64)methylclock_1.11.0.tgz(r-4.4-x86_64)methylclock_1.11.0.tgz(r-4.3-arm64)methylclock_1.11.0.tgz(r-4.3-x86_64)
methylclock_1.11.0.tar.gz(r-4.5-noble)methylclock_1.11.0.tar.gz(r-4.4-noble)
methylclock_1.11.0.tgz(r-4.4-emscripten)methylclock_1.11.0.tgz(r-4.3-emscripten)
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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

progress_data - PROGRESS cohor data
progress_vars - PROGRESS cohort variables

On BioConductor:methylclock-1.11.0(bioc 3.20)methylclock-1.10.0(bioc 3.19)

bioconductor-package

12 exports 0.82 score 286 dependencies

Last updated 2 months agofrom:bb5ccfa2d4

Exports:checkClocks checkClocksGA commonClockCpgs DNAmAge DNAmGA getCellTypeReference load_DNAm_Clocks_data load_DNAmGA_Clocks_data meffilEstimateCellCountsFromBetas meffilListCellTypeReferences plotCorClocks plotDNAmAge

Dependencies:abind annotate AnnotationDbi AnnotationForge AnnotationHub AnnotationHubData askpass backports base64 base64enc beanplot BH Biobase BiocBaseUtils BiocCheck BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biocViews biomaRt Biostrings bit bit64 bitops blob boot brew brio broom bslib bumphunter cachem callr car carData cellranger cli clipr cluster codetools colorspace commonmark confintr conflicted corrplot cowplot cpp11 crayon credentials curl data.table DBI dbplyr DelayedArray DelayedMatrixStats Deriv desc devtools diffobj digest doBy doRNG downlit dplyr dtplyr dynamicTreeCut ellipsis evaluate ExperimentHub ExperimentHubData fansi farver fastmap filelock fontawesome forcats foreach formatR fs futile.logger futile.options gargle genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery gert ggplot2 ggpmisc ggpp ggpubr ggrepel ggsci ggsignif gh gitcreds glue googledrive googlesheets4 graph gridExtra gtable haven HDF5Array highr hms htmltools htmlwidgets httpuv httr httr2 ids illuminaio impute ini IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lifecycle limma lme4 lmodel2 locfit lubridate magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mclust memoise methylclockData mgcv microbenchmark mime minfi miniUI minqa modelr multcomp multcompView multtest munsell mvtnorm nlme nloptr nnet nor1mix numDeriv openssl OrganismDbi pbkrtest PerformanceAnalytics pillar pkgbuild pkgconfig pkgdown pkgload planet plogr plyr png polynom praise preprocessCore prettyunits processx profvis progress promises ps purrr quadprog quantreg R.methodsS3 R.oo R.utils R6 ragg rappdirs RBGL rcmdcheck RColorBrewer Rcpp RcppEigen RCurl readr readxl rematch rematch2 remotes reprex reshape restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rngtools roxygen2 RPMM rprojroot Rsamtools RSQLite rstatix rstudioapi rtracklayer RUnit rversions rvest S4Arrays S4Vectors sandwich sass scales scrime selectr sessioninfo shiny siggenes snow sourcetools SparseArray SparseM sparseMatrixStats splus2R statmod stringdist stringi stringr SummarizedExperiment survival sys systemfonts testthat textshaping TH.data tibble tidyr tidyselect tidyverse timechange tinytex txdbmaker tzdb UCSC.utils urlchecker usethis utf8 uuid vctrs viridisLite vroom waldo whisker withr xfun XML xml2 xopen xtable xts XVector yaml zip zlibbioc zoo

Chronological and gestational DNAm age estimation using different methylation-based clocks

Institute for Global Health (ISGlobal), Barcelona, Spain Bioinformatics Research Group in Epidemiolgy (BRGE) http://brge.isglobal.org

Rendered frommethylclock.Rmdusingknitr::rmarkdownon Jul 04 2024.

Last update: 2022-07-11
Started: 2019-03-15

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

Package: methylclock 1.11.0

methylclock: Methylclock - DNA methylation-based clocks

Chronological and gestational DNAm age estimation using different methylation-based clocks

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)