horvath_clock

R tutorial for DNA methylation age and the epigenetic clock

Adapted for 450K array data by using the common 350 age-predictive CpG probes instead of 353

Source, R scripts and data are modified from the "R Tutorials" section

Analysis.R - R code from TUTORIAL1.docx that predicts age using data from a probes X samples CSV file, where the first column is ProbeID. Example: 27K data MethylationDataExample55.csv. Output: Output.csv with the columns:

• SampleID - sample identifier
• DNAmAge - DNA methylation age` - predicted age
• Comment - a comment if a sample looks suspicious
• noMissingPerSample - number of missing beta values per sample
• meanMethBySample, minMethBySample - the mean and min beta value before normalization
• predictedGender - predicted gender based on the mean across the X chromosomal markers
• meanXchromosome - mean beta value across the X chromosomal markers