Contains code to calibrate an epigenetic clock using either leave-one-out cross validation or leave-one-individual-out cross validation. Our examples is based on methylation information gained using a customised Illumina Infinium chip, targeting highly conserved CpG sites across mammals. The chip is described here: https://doi.org/10.1038/s41467-022-28355-z We used data of Indo-Pacific bottlenose dolphins (Tursiops aduncus). More details on the approaches and the code are provided in the code file.
We also provide an example of how to apply a calibrated epigenetic clock to samples of unknown epigenetic or chronological age.
To assess if epigenetic age is influenced by social variables, we employed permutated linear mixed models. Details are provided in the code file itself.
Example files for both codes can be found in the supplementary materal of our publication: (to be inserted).