getClock: Retrieve 'epigenetic clock' models
In biscuiteer: Convenience Functions for Biscuit

Description Usage Arguments Details Value Examples

Biscuiteer supports several 'epigenetic clock' models. This function retrieves the various models.

getClock(
  model = c("horvath", "horvathshrunk", "hannum", "skinandblood"),
  padding = 15,
  genome = c("hg19", "hg38", "GRCh37", "GRCh38"),
  useENSR = FALSE,
  useHMMI = FALSE
)

`model`	One of "horvath", "horvathshrunk", "hannum", or "skinandblood"
`padding`	How many base pairs (+/-) to expand a feature's footprint (DEFAULT: 15)
`genome`	One of "hg19", "GRCh37", "hg38", or "GRCh38" (DEFAULT: "hg19")
`useENSR`	Substitute ENSEMBL regulatory feature boundaries? (DEFAULT: FALSE)
`useHMMI`	Substitute HMM-based CpG island boundaries? (DEFAULT: FALSE)

The remapped coordinates for the Horvath (2012) and Hannum (2013) clocks, along with shrunken Horvath (2012) and improved Horvath (2018) models, are provided as part of biscuiteer (visit inst/scripts/clocks.R to find out how) along with some functionality to make them more usable in RRBS/WGBS data of varying coverage along varying genomes. For example, the HMM-based CpG island model introduced by Wu (2010) can be used to assign to within-island features the methylation rate of their associated island, and ENSEMBL regulatory build features (ENSR features, for short) such as CTCF binding sites can have their coordinates substituted for the default padded boundaries of a feature.

The net result of this process is that, while the default settings simply swap in a 30-bp stretch centered on the selected clock's CpG (and/or CpH) loci, add the intercept, and ship out the model, much more flexibility is available to the user. This function provides a single point for tuning of such options in the event that defaults don't work well for a user.

The precedence of options is as follows:

If a feature has neither ENSR nor HMMI IDs, it is padded (only) +/- bp.
If it has an HMMI but not ENSR ID or ENSR==FALSE, the HMM island is used.
If a feature has an ENSR ID, and ENSR==TRUE, the ENSR feature is used.

If a feature has both an ENSR ID and an HMMI ID, and both options are TRUE, then the ENSR start and end coordinates will take precedence over its HMMI.

The above shenanigans produce the GRanges object returned as gr in a List. The intercept value returned with the model is its fixed (B0) coefficient. The cleanup function returned with the model transforms its raw output.