added performance testing scripts

performance_testing/R_parse_timing_script.R

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+# Note. '/path/with/gctx/files/to/test/*gct*' refers to a directory of GCT and/or GCTx files to time parsing operations on.
+
+library(cmapR)
+
+# for storing timing results
+input_filenames <- c()
+parse_times <-c()
+
+# get all GCT and/or GCTx files in directory 
+input_files <- list.files(path="/path/with/gctx/files/to/test", 
+                          pattern="*.gct*", 
+                          full.names=TRUE,
+                          recursive=FALSE)
+
+for (f in input_files) {
+  start_time <- Sys.time()
+  in_gctoo <- parse.gctx(f)
+  end_time <- Sys.time()
+  elapsed_time <- end_time - start_time
+
+  input_filenames <- c(input_filenames, f)
+  parse_times <- c(parse_times, elapsed_time)
+}
+
+parse_timing_df <- as.data.frame(cbind(input_filenames, parse_times))
+write.table(parse_timing_df, "R_parsing_results.txt", sep="\t", quote=FALSE, row.names = FALSE)

performance_testing/R_write_timing_script.R

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+# '/path/to/large/gctx/file' refers to a large GCTX file (any size above 10174x100000 should work) from which file subsets are made.
+# In testing, the large GCTX file used lacked metadata; including metadata would cause slight variation in results.
+# Cache was cleared in between consecutive operations.
+
+library(cmapR)
+
+in_filenames = c()
+gct_write_results = c()
+gctx_write_results = c()
+
+large_gctx = parse.gctx("/path/to/large/gctx/file")
+
+col_spaces = c(96, 384, 1536, 3000, 6000, 12000, 24000, 48000, 100000)
+row_spaces = c(978, 10174)
+
+for (c in col_spaces) {
+  for (r in row_spaces) {
+    curr_gctoo = subset.gct(large_gctx, rid = 1:r, cid = 1:c)
+    out_fname = paste("write_test_n", paste(c, r, sep="x"), sep="_")
+
+    # gctx writing
+    start = Sys.time()
+    write.gctx(curr_gctoo, out_fname)
+    end = Sys.time()
+    gct_elapsed_time = end - start
+
+    # gct writing
+    start = Sys.time()
+    write.gct(curr_gctoo, out_fname)
+    end = Sys.time()
+    gctx_elapsed_time = end - start
+
+    in_filenames = c(in_filenames, paste(c, r, sep="x"))
+    gct_write_results = c(gct_write_results, gct_elapsed_time)
+    gctx_write_results = c(gctx_write_results, gctx_elapsed_time)
+  }
+}
+
+write_results_df = as.data.frame(cbind(in_filenames, gct_write_results, gctx_write_results))
+write.table(write_results_df, "R_writing_results.txt", sep="\t", quote=FALSE, row.names=FALSE)