Files

sampleAligner

Use the helper function created in this file to align the methylation data with the patient information and cell fractions.

groupProbes

Finds the most significant probes for different group stratification.

dmctFinder

Calculates the differentially methylated cell-type specific probes based on cell fraction using CellDMC.

cellAge

Uses the DMCTs to calculate the epigenetic ages of each cell type across all samples.

Workflow

1. Load Data

Call the fileAligner to get both the patient information file and the methylation data for the respective patients.

2. Distinguish Phentotype Groups

Separate into the the groups of each phenotype you wish to investigate the cell type fractions for.

3. Run CellDMC

Input the methylation data (n_samples, n_features), list of phenotypes (n_samples), and fraction (n_samples x n_features).

4. Extract Cell-specific CpG Sites

For each cell type collect their corresponding DMCTs if present.

5. Calculate Coefficients

Run through elastic net regularization model to find coefficients.

6. Calculate Cell Age

Run coefficients & methylation data through Horvath Clock.

Requirements

ggplot2
magrittr
dplyr
ggbeeswarm
broom
ggpubr
patchwork
data.table
EpiDISH
readr
data.table
ISLR
caret
glmnet