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Update run_calcPCClocks.R #7

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Update run_calcPCClocks.R #7

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6 changes: 4 additions & 2 deletions run_calcPCClocks.R
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Original file line number Diff line number Diff line change
Expand Up @@ -46,16 +46,18 @@ calcPCClocks <- function(path_to_PCClocks_directory, datMeth, datPheno){
#If needed: Fill in missing CpGs needed for calculation of PCs; use mean values from GSE40279 (Hannum 2013; blood)- note that for other tissues you might prefer to use a different one
datMeth <- as.data.frame(datMeth)
missingCpGs <- c(CpGs[!(CpGs %in% colnames(datMeth))])
if (length(missingCpGs)>0) {
datMeth[,missingCpGs] <- NA
for(i in 1:length(missingCpGs)){
datMeth[,missingCpGs[i]] <- imputeMissingCpGs[missingCpGs[i]]
}
}}

#fill in CpGs that are NA for all values
missingCpGs <- CpGs[apply(datMeth[,CpGs], 2, function(x)all(is.na(x)))]
if (length(missingCpGs)>0) {
for(i in 1:length(missingCpGs)){
datMeth[,missingCpGs[i]] <- imputeMissingCpGs[missingCpGs[i]]
}
}}
message("Any missing CpGs successfully filled in (see function for more details)")

#Prepare methylation data for calculation of PC Clocks (subset to 78,464 CpGs and perform imputation if needed)
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