Package: MEAT 1.25.0

Sarah Voisin

MEAT: Muscle Epigenetic Age Test

This package estimates epigenetic age in skeletal muscle, using DNA methylation data generated with the Illumina Infinium technology (HM27, HM450 and HMEPIC).

Authors:Sarah Voisin [aut, cre], Steve Horvath [ctb]

MEAT_1.25.0.tar.gz
MEAT_1.25.0.zip(r-4.7)MEAT_1.25.0.zip(r-4.6)MEAT_1.25.0.zip(r-4.5)
MEAT_1.25.0.tgz(r-4.6-any)MEAT_1.25.0.tgz(r-4.5-any)
MEAT_1.25.0.tar.gz(r-4.7-any)MEAT_1.25.0.tar.gz(r-4.6-any)
MEAT_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MEAT/json (API)

# Install 'MEAT' in R:

install.packages('MEAT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sarah-voisin/meat/issues

Datasets:

CpGs_in_MEAT - Description of the CpGs used in MEAT
CpGs_in_MEAT2.0 - Description of the CpGs used in MEAT2.0
elasticnet_model_MEAT - Elastic net model used in the original muscle clock (MEAT).
elasticnet_model_MEAT2.0 - Elastic net model used in the updated muscle clock (MEAT 2.0).
gold.mean.MEAT - Mean methylation in dataset GSE50498 reduced to the 19,401 CpGs of MEAT
gold.mean.MEAT2.0 - Mean methylation in dataset GSE50498 reduced to the 18,747 CpGs of MEAT 2.0
GSE121961 - GSE121961 methylation data
GSE121961_pheno - GSE121961 phenotypes

On BioConductor:MEAT-1.25.0(bioc 3.24)MEAT-1.24.0(bioc 3.23)

epigenetics dnamethylation microarray normalization biomedicalinformatics methylationarray preprocessing

5.30 score 1 stars 4 scripts 14 mentions 3 exports 174 dependencies

Last updated from:415382406b. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	371
linux-devel-x86_64	WARNING	669
source / vignettes	OK	498
linux-release-x86_64	WARNING	682
macos-release-arm64	WARNING	430
macos-oldrel-arm64	WARNING	465
windows-devel	WARNING	522
windows-release	WARNING	486
windows-oldrel	WARNING	477
wasm-release	OK	361

Exports:BMIQcalibration clean_beta epiage_estimation

Dependencies:abind affy affyio annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cigarillo cli clipr cluster codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dir.expiry doRNG dplyr dynamicTreeCut evaluate farver fastmap FDb.InfiniumMethylation.hg19 filelock foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glmnet glue gtable h5mread HDF5Array highr hms httr httr2 IlluminaHumanMethylation450kanno.ilmn12.hg19 illuminaio impute IRanges isoband iterators jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lifecycle limma locfit lumi magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise methylumi mgcv mime minfi multtest nleqslv nlme nor1mix openssl org.Hs.eg.db pillar pkgconfig plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl readr rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools ROC RPMM Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors S7 scales scrime selectr Seqinfo shape siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect TxDb.Hsapiens.UCSC.hg19.knownGene tzdb UCSC.utils utf8 vctrs viridisLite vroom wateRmelon withr xfun XML xml2 xtable XVector yaml

MEAT (Muscle Epigenetic Age Test)

Rendered fromMEAT.Rmdusingknitr::knitr

Last update: 2021-08-12
Started: 2020-01-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calibrate methylation data to a gold standard.	BMIQcalibration
Clean beta-matrix.	clean_beta
Description of the CpGs used in MEAT	CpGs_in_MEAT
Description of the CpGs used in MEAT2.0	CpGs_in_MEAT2.0
Elastic net model used in the original muscle clock (MEAT).	elasticnet_model_MEAT
Elastic net model used in the updated muscle clock (MEAT 2.0).	elasticnet_model_MEAT2.0
Estimates age in skeletal muscle from calibrated DNA methylation profiles.	epiage_estimation
Mean methylation in dataset GSE50498 reduced to the 19,401 CpGs of MEAT	gold.mean.MEAT
Mean methylation in dataset GSE50498 reduced to the 18,747 CpGs of MEAT 2.0	gold.mean.MEAT2.0
GSE121961 methylation data	GSE121961
GSE121961 phenotypes	GSE121961_pheno