#546 Updating days_to_follow_up and vital status

Should we add a parameter to control this update?

Author: Tiago Silva

R/clinical.R

@@ -540,6 +540,22 @@ GDCprepare_clinic <- function(
             clin$primary_pathology <- NULL
         }
 
+        # Update clinical data with follow-ups: days_to_last_followup and vital_status
+        message("Updating days_to_last_followup and vital_status from follow_up information using last entry")
+        followup <- parseFollowup(files,xpath,clinical.info)
+
+        followup_last <- followup %>% dplyr::group_by(bcr_patient_barcode) %>% dplyr::summarise(
+            days_to_last_followup = max(as.numeric(days_to_last_followup),na.rm = TRUE),
+            vital_status = vital_status[
+                ifelse(
+                    any(followup$days_to_last_followup %in% ""),
+                    which(followup$days_to_last_followup %in% ""),
+                    which.max(days_to_last_followup)
+                )
+            ]
+        )
+        clin$days_to_last_followup <- followup_last$days_to_last_followup[match(clin$bcr_patient_barcode,followup_last$bcr_patient_barcode)]
+        clin$vital_status <- followup_last$vital_status[match(clin$bcr_patient_barcode,followup_last$bcr_patient_barcode)]
     }
 
     if (tolower(clinical.info) == "sample") {