getRequiredProbes: View key probes involved in calculating DunedinPACE

In danbelsky/DunedinPACE: Dunedin Pace of Aging Methylation Score Calculator based on Dunedin Age 45 data (DunedinPACE)

View key probes involved in calculating DunedinPACE

Description

Returns a list containing the IDs of the probes needed for each Dunedin Pace of Aging Methylation Score Model. By default does not include all the required probes (20k) used in the normalization and DunedinPACE calculation.

Usage

getRequiredProbes(backgroundList=F)

Arguments

backgroundList

Default = FALSE. If set to true, it will return the full set of 20,000 probes in the background set used for normalization

Details

The 'PACEProjector' uses data from 20,000 CpGs. This includes 173 probes for PACE projection, and a background list that is used for normalization. We do not recommend using 'getRequiredProbes(backgroundList=F)' to pre-select a subset of probes for the 'PACEProjector' function, as this excludees the 19827 probes used for normalization and and could affect DunedinPACE estimates. If you need to pre-select probes, be sure to use 'getRequiredProbes(backgroundList=TRUE)'.

References

Belsky DW, Caspi A, Corcoran DL, Sugden K, Poulton R, Arseneault L, Baccarelli A, Chamarti K, Gao X, Hannon E, et al. 2022. DunedinPACE, a DNA methylation biomarker of the pace of aging. Deelen J, editor. eLife. 11:e73420. doi:10.7554/eLife.73420.

Examples

getRequiredProbes()

danbelsky/DunedinPACE documentation built on Feb. 24, 2024, 7:16 p.m.