Seabird epigenetic age assay - variable selection

• Main Authors: De Paoli-Iseppi, Ricardo, Deagle, Bruce, Polanowski, Andrea, McMahon, Clive, Dickinson, Joanne, Hindell, Mark, Jarman, Simon
• Format: Dataset
• Language: unknown
• Published: 2018
• Subjects: Age; Birds; DNA methylation; Epigenetics; DREAM; Flinders; Lambda; Fisher Island
• Online Access: http://hdl.handle.net/10255/dryad.197026; https://doi.org/10.5061/dryad.n4h3672/4

This R script uses the data frame of DNAm values from the pipeline script as an input to the glmnet package to select for markers based on lambda 1se or min. First, samples are adjusted for any between run difference and the cv.glmnet function is used to penalise the large set of variables against known age. Any selected variables are then visualised (and filtered if needed) using simple linear regression. The final selection of markers are then used to train and test a multiple linear regression.