Skip to content

Update run_calcPCClocks.R #7

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
kveeramah wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Update run_calcPCClocks.R #7

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 4 additions & 2 deletions run_calcPCClocks.R
View file
Open in desktop
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)
Expand Down