Calculate_PC_Cutoff.R

### Function calculating number of PCs to be kept for batch identification and correction
# threshold for N of PCs: start at PC1 and keep including PCs until drop in explained variance from PCi to PCi+2 < 1%
# if threshold >2, include first 2 PCs (needed for plots)
# include max 10 PCs

pc_cutoff <- function(data){
  for(i in 1:nrow(data)) {
    if(i > 10) break
    else if((data[i,]$var_explained - data[i + 2,]$var_explained) >=1) PC_number <- i 
    else if(PC_number < 2) PC_number = 2
    else break
  }
  return(PC_number)
}