Merge pull request #219 from KristinaGomoryova/remove_noise_update

remove_noise function updated

R/remove_noise.R

@@ -60,6 +60,7 @@ load_data <- function(filename,
 #' @param intensity_weighted Whether to use intensity to weight mass density estimation.
 #' @param do.plot Indicates whether plot should be drawn.
 #' @param cache Whether to use cache
+#' @param grouping_threshold The maximum difference between two scans to be considered the same EIC. Default is Inf. 
 #' @return A matrix with four columns: m/z value, retention time, intensity, and group number.
 #' @export
 remove_noise <- function(filename,
@@ -70,7 +71,8 @@ remove_noise <- function(filename,
                      baseline_correct_noise_percentile,
                      intensity_weighted,
                      do.plot,
-                     cache) {
+                     cache,
+                     grouping_threshold = Inf) {
   raw.data <- load_file(filename)
 
   raw.prof <- adaptive.bin(
@@ -87,10 +89,28 @@ remove_noise <- function(filename,
     raw.prof$features$intensities,
     raw.prof$features$grps
   )
-  
+
   run.sel <- raw.prof$height.rec[which(raw.prof$height.rec[, 2] >= raw.prof$min.count.run * min_pres & raw.prof$height.rec[, 3] > baseline_correct), 1]
 
   newprof <- newprof[newprof[, 4] %in% run.sel, ]
+
+  if (grouping_threshold < Inf) {
+    sorted_newprof <- newprof[order(newprof[,2]),]
+    new_grps <- cumsum(c(0, diff(sorted_newprof[,2])) > grouping_threshold)
+    sorted_newprof <- cbind(sorted_newprof, new_grps, deparse.level = 0)
+
+    sorted_newprof_df <- tibble::as_tibble(sorted_newprof)
+
+    newprof <- as.matrix(sorted_newprof_df |>
+      dplyr::group_by(V4, V5) |>
+      dplyr::mutate(cluster = cur_group_id()) |>
+      dplyr::ungroup() |>
+      dplyr::arrange(cluster) |>
+      dplyr::select(-V4, -V5)
+    )
+    colnames(newprof) <- NULL
+  }
+
   new.prof <- run_filter(
     newprof,
     min_pres = min_pres,

conda/environment-dev.yaml

@@ -5,16 +5,16 @@ channels:
   - defaults
 dependencies:
   - r-base
-  - icu <=70.1
+  - icu
   - r-mass
   - r-rgl
-  - bioconductor-mzR ==2.28.0
+  - bioconductor-mzR ==2.36.0
   - r-splines2
   - r-doparallel
   - r-foreach
   - r-snow
   - r-rcpp
-  - r-arrow >=7.0.0,<10.0.0
+  - r-arrow
   - r-dplyr
   - r-tidyr
   - r-stringr

tests/remote-files/input.txt

@@ -6,4 +6,5 @@ https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/
 https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/RCX_08_shortened.mzML
 https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/single_eic.mzml
 https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/alg3.mzdata
-https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/test_file.mzXML
+https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/test_file.mzXML
+https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/Tribrid_201106_009-QC1_1_NEG_FISABIO_single_eic.raw.mzML

tests/testthat/test-load.lcms.R

@@ -10,6 +10,10 @@ create_test_case <- function(filename, mz_length, rt_length, intensities_length)
 patrick::with_parameters_test_that(
   "test load.lcms reads different file types",
   {
+    if(packageVersion("mzR") >= "2.29.0" && tools::file_ext(filename) == "mzdata") {
+      print("mzR >= 2.29.0 no longer supports mzdata.")
+      skip()
+    }
     # Arrange: Set up test inputs
     testdata <- file.path("..", "testdata")
     input_path <- file.path(testdata, "input", filename)

tests/testthat/test-remove_noise.R

@@ -74,3 +74,33 @@ patrick::with_parameters_test_that(
     )
   )
 )
+
+test_that("remove noise works with grouping threshold", {
+  testdata <- file.path("..", "testdata")
+  input_path <- file.path(testdata,
+                          "input",
+                          "Tribrid_201106_009-QC1_1_NEG_FISABIO_single_eic.raw.mzML")
+
+  expected <- tibble(group_number = c(1, 2, 3, 5, 6, 7, 8, 9),
+                     n = c(67, 73, 3, 39, 2, 6, 3, 7))
+
+  sut <- remove_noise(
+    input_path,
+    min_pres = 0.8,
+    min_run = 0.2,
+    mz_tol = 5e-05,
+    baseline_correct = 0.0,
+    baseline_correct_noise_percentile = 0.05,
+    intensity_weighted = FALSE,
+    do.plot = FALSE,
+    cache = FALSE,
+    grouping_threshold = 4
+  )
+
+  actual <- sut %>%
+    mutate(group = factor(group_number)) %>%
+    group_by(group_number) %>%
+    summarize(n = n())
+
+  expect_equal(actual, expected)
+})