Skip to content

A bug-free version of calcPCBrainAge #3

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
xr-song wants to merge 1 commit into
base: main
Choose a base branch
from
Open

A bug-free version of calcPCBrainAge #3

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
23 changes: 10 additions & 13 deletions R/calcPCBrainAge.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,16 +35,23 @@ calcPCBrainAge <- function(DNAm, pheno = NULL, CpGImputation = NULL){
###################################################
### Check if all necessary CpGs are in the data ###
###################################################

# Debug: convert input data to data.frame if it's a matrix
if (is.matrix(DNAm)) {
DNAm <- as.data.frame(DNAm)
message("Input matrix is converted to a data frame.")
}

missingCpGs <- rownames(PCBrainAge_Model$rotation)[!(rownames(PCBrainAge_Model$rotation) %in% colnames(DNAm))]
DNAm[,missingCpGs] <- NA
if(!is.na(missingCpGs[1])){ #if there are columns of CpGs missing...
if(is.null(CpGImputation)){ #...and the user didn't specify a mean CpG vector, use the Hannum 2013 blood mean data
data("imputeMissingBrainCpGs")
for(i in 1:length(missingCpGs)){
datMeth[,missingCpGs[i]] <- imputeMissingBrainCpGs[missingCpGs[i]]
DNAm[,missingCpGs[i]] <- imputeMissingBrainCpGs[missingCpGs[i]]
}} else{ #...otherwise use the user's mean CpG vector which contains the required CpG values
for(i in 1:length(missingCpGs)){
datMeth[,missingCpGs[i]] <- CpGImputation[missingCpGs[i]]
DNAm[,missingCpGs[i]] <- CpGImputation[missingCpGs[i]]
}
}
}
Expand All @@ -54,7 +61,7 @@ calcPCBrainAge <- function(DNAm, pheno = NULL, CpGImputation = NULL){
DNAm <- DNAm[,match(rownames(PCBrainAge_Model$rotation), colnames(DNAm))]

if(any(is.na(DNAm))){
DNAm <- apply(DNAm,2,meanimpute)
DNAm <- apply(DNAm,2,meanImpute) # Debug: call the function meanImpute
message("Mean imputation successfully completed for missing CpG values")
}

Expand All @@ -73,13 +80,3 @@ calcPCBrainAge <- function(DNAm, pheno = NULL, CpGImputation = NULL){
pheno
}
}