The goal of prcPhenoAge is to perform a calculation of PhenoAge (2018) while subscoring the epigenetic age into the portion of PhenoAge reliant upon beta values annotated to be in PRC associated CpGs, and non-PRC associated CpGs. The determination of PRC-associated CpGs was desrived from Lee et al. (2006) PMID: 16630818.
You can install the released version of prcPhenoAge from GitHub with:
devtools::github_install("MorganLevineLab/prcPhenoAge")Here is a template code using example data (Lehne et al. 2015) available as part of this package:
library(prcPhenoAge)
data("exampleBetas")
data("examplePheno")
PRC_PhenoAge <- calcnonPRCPhenoAge(exampleBetas, examplePheno, imputation = F)
PRC_PhenoAge <- calcPRCPhenoAge(exampleBetas, PRC_PhenoAge, imputation = F)
PRC_PhenoAge
#> name geo_accession gender age group sample nonPRC_PhenoAge
#> 1 7786915023_R02C02 GSM1343050 M 57.9 1 1 -26.98018
#> 2 7786915135_R04C02 GSM1343051 M 42.0 1 2 -34.64179
#> 3 7471147149_R06C01 GSM1343052 M 47.4 1 3 -35.04189
#> 4 7786915035_R05C01 GSM1343053 M 49.3 1 4 -33.56565
#> 5 7786923035_R01C01 GSM1343054 M 52.5 1 5 -37.31548
#> PRC_PhenoAge
#> 1 18.60933
#> 2 15.03647
#> 3 17.92249
#> 4 16.86863
#> 5 17.00389