Feature/refactor_DIMS_FillMissing_2

DIMS/preprocessing/fill_missing_functions.R

@@ -1,14 +1,15 @@
-fill_missing_intensities <- function(peakgroup_list, repl_pattern, thresh, not_random = FALSE) {
+fill_missing_intensities <- function(peakgroup_list, repl_pattern, thresh, disable_randomness = FALSE) {
   #' Replace intensities that are zero with random value
   #'
   #' @param peakgroup_list: Peak groups (matrix)
   #' @param repl_pattern: Replication pattern (list of strings)
   #' @param thresh: Value for threshold between noise and signal (integer)
+  #' @param thresh: Variable which indicates whether randomness should be disabled (boolean)
   #'
   #' @return final_outlist: peak groups with filled-in intensities (matrix)
 
   # for unit test, turn off randomness
-  if (not_random) {
+  if (disable_randomness) {
     set.seed(123)
   }
 

DIMS/tests/testthat/fixtures/test_peakgroup_list.txt

@@ -0,0 +1,6 @@
+"mzmed.pgrp"	"nrsamples"	"ppmdev"	"assi_HMDB"	"all_hmdb_names"	"iso_HMDB"	"HMDB_code"	"all_hmdb_ids"	"sec_hmdb_ids"	"theormz_HMDB"	"C101.1"	"C102.1"	"P2.1"	"P3.1"	"avg.int"	"assi_noise"	"theormz_noise"	"avg.ctrls"	"sd.ctrls"	"C101.1_Zscore"	"C102.1_Zscore"	"P2.1_Zscore"	"P3.1_Zscore"
+"1"	300.199680958642	0.451108327135444	0.111112214857712	NA	"NA;NA"	NA	"HMDB1234567"	"HMDB1234567;HMDB1234567"	NA	NA	1000	5000	10000	50000	NA	NA	NA	NA	NA	9000	13000	90000	130000
+"2"	300.000315890415	0.498603057814762	0.473299680976197	NA	"NA;NA"	NA	"HMDB1234567_1"	"HMDB1234567_1;HMDB1234567_1"	NA	NA	2000	6000	20000	60000	NA	NA	NA	NA	NA	10000	14000	1e+05	140000
+"3"	300.254185894039	0.589562055887654	0.17426158930175	NA	"NA;NA"	NA	"HMDB1234567_2"	"HMDB1234567_2;HMDB1234567_2"	NA	NA	3000	7000	30000	70000	NA	NA	NA	NA	NA	11000	15000	110000	150000
+"4"	300.755745105678	0.277923040557653	0.186787674436346	NA	"NA;NA"	NA	"HMDB1234567_7"	"HMDB1234567_7;HMDB1234567_7"	NA	NA	4000	8000	40000	80000	NA	NA	NA	NA	NA	12000	16000	120000	160000
+

DIMS/tests/testthat/test_fill_missing.R

@@ -4,24 +4,18 @@ source("../../preprocessing/fill_missing_functions.R")
 
 # test fill_missing_intensities
 testthat::test_that("missing values are corretly filled with random values", {
-  # create peakgroup_list to test on in diagnostics setting
-  test_peakgroup_list <- data.frame(matrix(NA, nrow = 4, ncol = 23))
-  colnames(test_peakgroup_list) <- c("mzmed.pgrp", "nrsamples", "ppmdev", "assi_HMDB", "all_hmdb_names",
-                                     "iso_HMDB", "HMDB_code", "all_hmdb_ids", "sec_hmdb_ids", "theormz_HMDB",
-                                     "C101.1", "C102.1", "P2.1", "P3.1",
-                                     "avg.int", "assi_noise", "theormz_noise", "avg.ctrls", "sd.ctrls",
-                                     "C101.1_Zscore", "C102.1_Zscore", "P2.1_Zscore", "P3.1_Zscore")
-  test_peakgroup_list[, c(1)] <- 300 + runif(4)
-  test_peakgroup_list[, c(2, 3)] <- runif(8)
-  test_peakgroup_list[, "HMDB_code"] <- c("HMDB1234567", "HMDB1234567_1", "HMDB1234567_2", "HMDB1234567_7")
-  test_peakgroup_list[, "all_hmdb_ids"] <- paste(test_peakgroup_list[, "HMDB_code"],
-                                                 test_peakgroup_list[, "HMDB_code"], sep = ";")
-  test_peakgroup_list[, "all_hmdb_names"] <- paste(test_peakgroup_list[, "assi_HMDB"],
-                                                   test_peakgroup_list[, "assi_HMDB"], sep = ";")
-  test_peakgroup_list[, grep("C", colnames(test_peakgroup_list))] <- 1000 * (1:16)
-  test_peakgroup_list[, grep("P", colnames(test_peakgroup_list))] <- 0
+  # It's necessary to copy/symlink the files to the current location for the fill_missing_intensities function
+  test_files <- list.files("fixtures/", "test_peakgroup_list", full.names = TRUE)
+  file.symlink(file.path(test_files), getwd())
+
+  # create replication pattern of technical replicates
   test_repl_pattern <- c(list(1), list(2), list(3), list(4))
   names(test_repl_pattern) <- c("C101.1", "C102.1", "P2.1", "P3.1")
+
+  # read in peakgroup_list, set intensities for patient columns to zero
+  test_peakgroup_list <- read.table("./test_peakgroup_list.txt", sep= "\t")
+  test_peakgroup_list[, grep("P", colnames(test_peakgroup_list))] <- 0
+
   test_thresh <- 2000
 
   # create a large peak group list to test for negative values
@@ -32,14 +26,11 @@ testthat::test_that("missing values are corretly filled with random values", {
   # for the sake of time, leave only one intensity column with zeros
   test_large_peakgroup_list$P2.1 <- 1
 
-  expect_equal(round(fill_missing_intensities(test_peakgroup_list, test_repl_pattern, test_thresh, not_random = TRUE)$P2.1),
+  expect_equal(round(fill_missing_intensities(test_peakgroup_list, test_repl_pattern, test_thresh, disable_randomness = TRUE)$P2.1),
                c(1944, 1977, 2156, 2007), TRUE, tolerance = 0.1)
   # fill_missing_intensities should not produce any negative values, even if a large quantity of numbers are filled in
-  start.time <- Sys.time()
-  expect_gt(min(fill_missing_intensities(test_large_peakgroup_list, test_repl_pattern, test_thresh, not_random = FALSE)$P3.1),
+  expect_gt(min(fill_missing_intensities(test_large_peakgroup_list, test_repl_pattern, test_thresh, disable_randomness = FALSE)$P3.1),
             0, TRUE)
-  end.time <- Sys.time()
-  time.taken <- end.time - start.time
-  time.taken
 
 })
+