DNA-m Age Calculation

Running existing models to estimate age from CpG methylation samples.

Example run

With cargo installed, compile and run:

$ cargo run -- examples/GSM2122878-57726.csv
   Compiling dnam v0.1.0 (DNAm)
    Finished dev [unoptimized + debuginfo] target(s) in 1.73s
     Running `target/debug/dnam examples/GSM2122878-57726.csv`
Horvath Clock : 17.73 years
DNAm PhenoAge : 37.79 years

Or compile once and then run:

$ cargo build --release
$ ./target/release/dnam examples/GSM2122878-57726.csv
Horvath Clock : 17.73 years
DNAm PhenoAge : 37.79 years

Notes:

• There is no normalization of the CpG values.
• There's no imupation of missing values (they are treated as zero)

Sources

Horvath

• https://www.ncbi.nlm.nih.gov/pubmed/30048243
• Coefficients are in Supplementary dataset 2, but I've taken them from http://clockbio.com/cpg-coefficients/ (the file CpG-coefficients.csv)

Phenoage

• https://www.ncbi.nlm.nih.gov/pubmed/29676998
• Coefficients are in Supplementary dataset 2, but I've taken them from http://clockbio.com/wp-content/uploads/2018/08/coef_pheno.csv

Clues

If you have a tab separated file (e.g., from the Gene Expression Omnibus), you'll need to remove extra headers and convert the tabs into commas. For example:

$ tail +3 GSMxxxx.txt | xsv fmt -d '\t' > GSMxxxx.csv