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

# 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-1.19.0(bioc 3.24)methylclock-1.18.0(bioc 3.23)

dnamethylation biologicalquestion preprocessing statisticalmethod normalization cpp

5.83 score 54 stars 63 scripts 12 exports 291 dependencies

Last updated from:0fec6e84d9. Checks:2 ERROR, 11 WARNING, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	306
linux-devel-arm64	WARNING	545
linux-devel-x86_64	WARNING	758
source / vignettes	ERROR	534
linux-release-arm64	WARNING	562
linux-release-x86_64	WARNING	710
macos-release-arm64	WARNING	671
macos-release-x86_64	WARNING	903
macos-oldrel-arm64	WARNING	358
macos-oldrel-x86_64	WARNING	926
windows-devel	WARNING	844
windows-release	WARNING	812
windows-oldrel	WARNING	916
wasm-release	OK	329

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 biocmake BiocManager BiocParallel BiocVersion biocViews Biostrings bit bit64 bitops blob boot brew brio broom bslib bumphunter cachem callr car carData caTools cellranger cigarillo 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 dir.expiry doBy doRNG downlit dplyr dtplyr dynamicTreeCut ellipsis evaluate ExperimentHub ExperimentHubData fansi farver fastmap filelock fontawesome forcats foreach forecast formatR Formula fracdiff fs futile.logger futile.options gargle genefilter generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GEOquery gert ggplot2 ggpmisc ggpp ggpubr ggrepel ggsci ggsignif gitcreds glue googledrive googlesheets4 graph gridExtra gtable h5mread 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 lmtest locfit lubridate magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mclust memoise methylclockData mgcv mime minfi miniUI minqa modelr multtest nlme nloptr nnet nor1mix numDeriv openssl OrganismDbi otel pak pbkrtest PerformanceAnalytics pillar pkgbuild pkgconfig pkgdown pkgload planet plyr png polynom praise preprocessCore prettyunits processx profvis progress promises ps purrr quadprog quantreg R.methodsS3 R.oo R.utils R6 ragg rappdirs RBGL rbibutils rcmdcheck RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack readr readxl reformulas rematch rematch2 rentrez reprex reshape restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rngtools roxygen2 RPMM rprojroot Rsamtools RSQLite rstatix rstudioapi rtracklayer RUnit rversions rvest S4Arrays S4Vectors S7 sass scales scrime selectr Seqinfo sessioninfo shiny siggenes snow sourcetools SparseArray SparseM sparseMatrixStats splus2R statmod stringdist stringi stringr SummarizedExperiment survival sys systemfonts testthat textshaping tibble tidyr tidyselect tidyverse timechange timeDate tinytex tzdb UCSC.utils urca urlchecker usethis utf8 uuid vctrs viridisLite vroom waldo whisker withr xfun XML xml2 xopen xtable xts XVector yaml zip zoo

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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 1.19.0

methylclock: Methylclock - DNA methylation-based clocks

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