Weighted 2D-kernel density estimations provide a new probabilistic measure for epigenetic age - Additional files
Creators
- 1. Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- 2. Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
- 3. Institute for Computational Biomedicine - Disease Modeling, RWTH Aachen University, Aachen, Germany
- 4. Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- 5. Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
- 6. Institute for Computational Genomics, RWTH Aachen University Hospital, Aachen, Germany
- 7. Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
Description
This repository contains the following files:
Additional file 2: kernels.Rds. .Rds file containing the 27 kernels calculated with our algorithm for the 27 CpG clock (WKDE).
Additional file 3: best_parameters.Rds. .Rds file containing the 27 weights for the 27 CpG clock (WKDE).
Additional file 4: WKDE_functions.R. .R script containing the functions w2dkage (to calculate epigenetic age), w2dkrange (to calculate probability age functions) and w2dkvs (to calculate variation score) with the 27CpG WKDE method. All the 3 functions have one input: a matrix of DNAm beta values (CpGs in rows, samples in columns).
Additional file 5: WKDE_method_and_figures.R. R script containing the source code to load the training and validation datasets used in the 27CpG WKDE clock, to create an epigenetic clock by implementing the WKDE method using the training dataset, and to generate the main figures of the manuscript.
Files
Files
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