| title | author | date | package | output | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Introduction to R-package EpiMitClocks |
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2023-5-25 |
EpiMitClocks_0.1.0 |
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The purpose of the EpiMitClocks R-package is to provide functions for estimating the mitotic age of tissues from a corresponding DNA methylation (DNAm) profile. These functions are epigenetic mitotic clocks, providing separate mitotic age estimates on scales unique to each clock. So each estimate should be interpreted as a relative mitotic age, not an absolute one, except for the epiTOC2 clock which does aim to estimate the total number of stem-cell divisions in a tissue. Current version of the R-package, estimates mitotic age according to the following mitotic clocks: epiTOC, epiTOC2, HypoClock, RepliTali, epiCMIT and stemTOC. EpiMitClocks has been installed and tested on Ubuntu running R-version 4.3.1 and Windows10 running R-version 4.1.1 .
To install:
library(devtools)
devtools::install_github("aet21/EpiMitClocks")Alternatively, download the EpiMitClocks-master.zip file from the Code-link above and install locally from within R.
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DNA methylation loss in late-replicating domains is linked to mitotic cell division. Zhou W, Dinh HQ, Ramjan Z, Weisenberger DJ, Nicolet CM, Shen H, Laird PW, Berman BP. Nat Genet. 2018 Apr;50(4):591-602. doi: 10.1038/s41588-018-0073-4.
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Cell division drives DNA methylation loss in late-replicating domains in primary human cells. Endicott JL, Nolte PA, Shen H, Laird PW. Nat Commun. 2022 Nov 8;13(1):6659. doi: 10.1038/s41467-022-34268-8.
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