double check case selection numbers

2021-11-16_shawn_bladder_uhn_eligible_cases.R

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+# Description: Check BLADDER eligible case lists.  
+# Author: Haley Hunter-Zinck
+# Date: 2021-11-16
+
+# setup ----------------------------
+
+tic = as.double(Sys.time())
+
+library(glue)
+library(dplyr)
+library(synapser)
+synLogin()
+
+# synapse
+synid_file_old <- "syn22311993"
+synid_file_new <- "syn26467942"
+synid_file_mat <- "syn26467941"
+
+# functions ----------------------------
+
+#' Download and load data stored in csv or other delimited format on Synapse
+#' into an R data frame.
+#' 
+#' @param synapse_id Synapse ID
+#' @version Version of the Synapse entity to download.  NA will load current
+#' version
+#' @param set Delimiter for file
+#' @param na.strings Vector of strings to be read in as NA values
+#' @param header TRUE if the file contains a header row; FALSE otherwise.
+#' @param check_names TRUE if column names should be modified for compatibility 
+#' with R upon reading; FALSE otherwise.
+#' @return data frame
+get_synapse_entity_data_in_csv <- function(synapse_id, 
+                                           version = NA,
+                                           sep = ",", 
+                                           na.strings = c("NA"), 
+                                           header = T,
+                                           check_names = F) {
+
+  if (is.na(version)) {
+    entity <- synGet(synapse_id)
+  } else {
+    entity <- synGet(synapse_id, version = version)
+  }
+
+  data <- read.csv(entity$path, stringsAsFactors = F, 
+                   na.strings = na.strings, sep = sep, check.names = check_names,
+                   header = header)
+  return(data)
+}
+
+# read ----------------------------
+
+old <- get_synapse_entity_data_in_csv(synid_file_old)
+new <- get_synapse_entity_data_in_csv(synid_file_new)
+mat <- get_synapse_entity_data_in_csv(synid_file_mat)
+
+# main ----------------------------
+
+pt_old <- unlist(old %>% filter(is.na(remove)) %>% select(patient_id))
+pt_new <- new$PATIENT_ID
+
+print(length(pt_old))
+print(length(pt_new))
+print(length(intersect(pt_old, pt_new)))
+print(setdiff(pt_old, pt_new))
+print(setdiff(pt_new, pt_old))
+
+mat %>% 
+  filter(is.element(PATIENT_ID, setdiff(pt_new, pt_old)))
+
+# close out ----------------------------
+
+toc = as.double(Sys.time())
+print(glue("Runtime: {round(toc - tic)} s"))