look at derived variable components

2021-12-01_ritika_missing_rx_treatment_start.R

@@ -13,8 +13,9 @@ synLogin()
 
 # synapse
 synid_file_cbio <- "syn26349077"
-synid_file_der <- "syn25931923"
+synid_file_der_radtx <- "syn25931923"
 synid_table_rx <- "syn21446710"
+synid_table_dx <- "syn21446701"
 
 # parameters
 cohort = "PANC"
@@ -55,28 +56,33 @@ get_synapse_entity_data_in_csv <- function(synapse_id,
 
 # read ----------------------------
 
-data_der <- get_synapse_entity_data_in_csv(synid_file_der, sep = ",")
+data_der <- get_synapse_entity_data_in_csv(synid_file_der_radtx, sep = ",")
 data_cbio <- get_synapse_entity_data_in_csv(synid_file_cbio, sep = "\t")
 
-query <- glue("SELECT record_id, rt_start_time, rt_stop_time, rt_dose, rt_fractions, rt_total_dose FROM {synid_table_rx} WHERE cohort = '{cohort}'")
+query <- glue("SELECT record_id, rt_start_time, rt_stop_time, rt_dose, rt_fractions, rt_total_dose, rt_start_int, rt_end_int FROM {synid_table_rx} WHERE cohort = '{cohort}'")
 data_tbl <- as.data.frame(synTableQuery(query, includeRowIdAndRowVersion = F))
 
+str_ids <- paste0("'", paste0(patient_ids, collapse = "','"), "'")
+query <- glue("SELECT cohort, record_id, ca_cadx_int FROM {synid_table_dx} WHERE cohort = '{cohort}' AND record_id IN ({str_ids})")
+data_dx <- as.data.frame(synTableQuery(query, includeRowIdAndRowVersion = F))
+
 # main ----------------------------
 
 print("Table data:")
 print(data_tbl %>%
   filter(is.element(record_id, patient_ids)))
+print(data_dx)
 print("--------")
 
-print("Derived variable file: ")
+print("Derived radiation treatment variable file: ")
 print(data_der %>%
   filter(is.element(record_id, patient_ids)) %>%
-  select(record_id, rt_start_time, rt_stop_time, rt_dose, rt_fractions, rt_total_dose))
+  select(record_id, rt_start_time, rt_stop_time, rt_dose, rt_fractions, rt_total_dose, dx_rt_start_days, rt_start_int))
 print("--------")
 
 print("cBioPortal file:")
 print(data_cbio %>%
-  filter(is.element(PATIENT_ID, patient_ids) & is.na(START_DATE)) %>%
+  filter(is.element(PATIENT_ID, patient_ids) & !is.na(RT_TOTAL_DOSE)) %>%
   select(PATIENT_ID, START_DATE, STOP_DATE, RT_DOSE, RT_FRACTIONS, RT_TOTAL_DOSE))
 print("--------")