Fixed bug which caused isofiltr to fail is some subsection of input has no isotope pairs

R/IsoFiltR.R

@@ -353,6 +353,11 @@ merge_and_filter_abundances <- function(final_pair2, end_data) {
   return(aligned_data)
 }
 
+#' Return TRUE if any of the elements in the list has a length of 0, otherwise FALSE
+filtered_data_is_empty<- function(filtered_data) {
+  return(any(lapply(filtered_data, length) == 0))
+}
+
 #' Process carbon isotoping data
 #'
 #' This function processes carbon isotoping data using specified parameters and filtering criteria.
@@ -394,6 +399,13 @@ process_carbon_isotoping <- function(raw_data, carb_error, carb_ratio, end_data)
     extracted_pair$iso_pair
   )
 
+  if(filtered_data_is_empty(filtered_data)) {
+    return(list(
+      MonoC = raw_data, # treat all data as mono and return it.
+      IsoC1 = data.frame(Exp_mass = c(), Abundance = c(), RT = c()),
+      IsoC2 = data.frame(Exp_mass = c(), Abundance = c(), RT = c())))
+  }
+
   iso1 <- data.frame(Mono_mass = filtered_data$Iso_mass1, Tag = "Iso1")
   iso1 <- rbind(iso1, data.frame(Mono_mass = -42, Tag = "Iso1"))
 

tests/testthat/test-IsoFiltR.R

@@ -7,3 +7,23 @@ patrick::with_parameters_test_that("IsoFiltR works",
   },
   mode = c("pos", "neg")
 )
+
+test_that("IsoFiltR works on recetox-aplcms output", {
+  raw <- read.table(file.path("test-data", "21_qc_no_dil_milliq.txt"), header=TRUE, sep="\t")
+  expected_path <- file.path("test-data", "21_qc_no_dil_milliq_iso.rds")
+
+  actual <- IsoFiltR(raw)
+
+  expected <- readRDS(expected_path)
+  expect_equal(actual, expected)
+})
+
+patrick::with_parameters_test_that("filtered_data_is_empty works", {
+  expect_equal(filtered_data_is_empty(test_data), expected)
+
+  },
+  patrick::cases(
+    empty = list(test_data=list(content=c()), expected=TRUE),
+    not_empty = list(test_data=list(content=c(1,2,3)), expected=FALSE)
+  )
+)