Function for calculating appropriate number of PCs to include for bat…

…ch identification/correction

data/Calculate_PC_Cutoff.R

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+### 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)
+}