merge variable synopsis

2021-12-13_xindi_combine_variable_synopsis.R

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+# Description: combine BPC variable synopsis from multiple cohorts.
+# Author: Haley Hunter-Zinck
+# Date: 2021-12-13
+
+# setup ----------------------------
+
+tic = as.double(Sys.time())
+
+library(glue)
+library(dplyr)
+library(synapser)
+synLogin()
+
+# synapse
+synid_file_crc <- "syn26077307"
+synid_file_nsclc <- "syn26028547"
+synid_file_brca <- "syn26077309"
+synid_folder_output <- "syn26529348"
+
+# functions ----------------------------
+
+#' Read contents of an Excel Spreadsheet stored on Synapse.
+#' 
+#' @param synapse_id Synapse ID of the spreadsheet
+#' @param version Version of the file
+#' @param sheet Number of the sheet of the spreadsheet
+#' @param check.names Whether R should modify names if non-conforming
+#' @return Matrix of data
+#' @example 
+#' get_synapse_entity_data_in_xlsx(synapse_id = "syn123345", sheet = 2)
+get_synapse_entity_data_in_xlsx <- function(synapse_id, 
+                                            version = NA,
+                                            sheet = 1,
+                                            check.names = F) {
+  library(openxlsx)
+
+  if (is.na(version)) {
+    entity <- synGet(synapse_id)
+  } else {
+    entity <- synGet(synapse_id, version = version)
+  }
+
+  data <- read.xlsx(entity$path, check.names = check.names, sheet = sheet)
+
+  return(data)
+}
+
+#' Store a file on Synapse with options to define provenance.
+#' 
+#' @param path Path to the file on the local machine.
+#' @param parent_id Synapse ID of the folder or project to which to load the file.
+#' @param file_name Name of the Synapse entity once loaded
+#' @param prov_name Provenance short description title
+#' @param prov_desc Provenance long description
+#' @param prov_used Vector of Synapse IDs of data used to create the current
+#' file to be loaded.
+#' @param prov_exec String representing URL to script used to create the file.
+#' @return Synapse ID of entity representing file
+save_to_synapse <- function(path, 
+                            parent_id, 
+                            file_name = NA, 
+                            prov_name = NA, 
+                            prov_desc = NA, 
+                            prov_used = NA, 
+                            prov_exec = NA) {
+
+  if (is.na(file_name)) {
+    file_name = path
+  } 
+  file <- File(path = path, parentId = parent_id, name = file_name)
+
+  if (!is.na(prov_name) || !is.na(prov_desc) || !is.na(prov_used) || !is.na(prov_exec)) {
+    act <- Activity(name = prov_name,
+                    description = prov_desc,
+                    used = prov_used,
+                    executed = prov_exec)
+    file <- synStore(file, activity = act)
+  } else {
+    file <- synStore(file)
+  }
+
+  return(file$properties$id)
+}
+
+# read ----------------------------
+
+synop_crc <- get_synapse_entity_data_in_xlsx(synapse_id = synid_file_crc,
+                                             sheet = 2)
+synop_nsclc <- get_synapse_entity_data_in_xlsx(synapse_id = synid_file_nsclc,
+                                             sheet = 2)
+synop_brca <- get_synapse_entity_data_in_xlsx(synapse_id = synid_file_brca,
+                                             sheet = 2)
+
+
+# main ----------------------------
+
+synop_all <- bind_rows(bind_rows(synop_brca, synop_crc), synop_nsclc)
+idx_dup <- which(duplicated(synop_all$Variable.Name))
+
+synop_all <- synop_all[-idx_dup, ] %>%
+  mutate(BrCa = is.element(Variable.Name, synop_brca$Variable.Name)) %>%
+  mutate(CRC = is.element(Variable.Name, synop_crc$Variable.Name)) %>%
+  mutate(NSCLC = is.element(Variable.Name, synop_nsclc$Variable.Name)) %>%
+  select(Dataset, Variable.Name, Field.Label, Data.Type, Values, BrCa, CRC, NSCLC)
+
+# write ----------------------------
+
+file_output <- "BPC-consortium_variables_synopsis.xlsx"
+write.xlsx(synop_all, file = file_output, overwrite = T)
+
+save_to_synapse(path = file_output, 
+                parent_id = synid_folder_output,
+                prov_name = "merged variable synopsis", 
+                prov_desc = "variable synopsis from merging variable synopsis from BrCa, CRC, and NSCLC cohorts", 
+                prov_used = c(synid_file_brca, synid_file_crc, synid_file_nsclc), 
+                prov_exec = "https://github.com/hhunterzinck/genie_requests/blob/main/2021-12-13_xindi_combine_variable_synopsis.R")
+
+
+file.remove(file_output)
+
+# close out ----------------------------
+
+toc = as.double(Sys.time())
+print(glue("Runtime: {round(toc - tic)} s"))