methylclockData
This is the development version of methylclockData; for the stable release version, see methylclockData.
Data for methylclock package
Bioconductor version: Development (3.24)
Data resources used by the methylclock package to estimate chronological, gestational and biological age from DNA methylation, and to adjust those estimates for blood cell composition. It provides the coefficient tables of the individual clocks, the CpG sets of the mitotic counters, the weights of the neural network clock, and example methylation datasets. It also provides nine cell type reference datasets (andrews and bakulski cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete, combined cord blood, cord blood gse68456, gervin and lyle cord blood, guintivano dlpfc, saliva gse48472), downloaded from meffil (https://github.com/perishky/meffil/), which are used to estimate cell counts for the extrinsic epigenetic age acceleration (EEAA) method. All resources are served through ExperimentHub.
Author: Juan R. Gonzalez [aut], Dolors Pelegri-Siso [aut, cre]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri at isglobal.org>
citation("methylclockData")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("methylclockData")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("methylclockData")| References for metilclock using Bioconductor's ExperimentHub | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | ExperimentData, ExperimentHub, Homo_sapiens_Data, OrganismData, SpecimenSource, Tissue |
| Version | 1.21.3 |
| License | MIT + file LICENSE |
| Depends | |
| Imports | ExperimentHubData, ExperimentHub, utils |
| System Requirements | |
| URL | https://github.com/isglobal-brge/methylclockData |
| Bug Reports | https://github.com/isglobal-brge/methylclockData/issues |
See More
| Suggests | knitr, BiocStyle, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | methylclock |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | methylclockData_1.21.3.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/methylclockData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/methylclockData |
| Package Short Url | https://bioconductor.org/packages/methylclockData/ |
| Package Downloads Report | Download Stats |