Fix #166

R/annotate_spectra.R

@@ -116,7 +116,8 @@ annotate_spectra <- function(input = get_params(step = "annotate_spectra")$files
  cutoff = qutoff,
  dalton = dalton,
  polarity = polarity,
- ppm = ppm
+ ppm = ppm,
+ sanitize = FALSE
  ) |>
  lapply(FUN = applyProcessing) |>
  concatenateSpectra()

R/import_spectra.R

@@ -21,6 +21,7 @@ import::from(stringi, stri_replace_all_regex, .into = environment())
 #' @param dalton Dalton tolerance
 #' @param polarity Polarity
 #' @param ppm PPM tolerance
+#' @param sanitize Flag indicating whether to sanitize. Default TRUE
 #'
 #' @return Spectra object containing the imported spectra
 #'
@@ -31,7 +32,8 @@ import_spectra <- function(file,
  cutoff = 0,
  dalton = 0.01,
  polarity = NA,
- ppm = 10) {
+ ppm = 10,
+ sanitize = TRUE) {
  file_ext <-
  stri_replace_all_regex(
  str = file,
@@ -40,29 +42,17 @@ import_spectra <- function(file,
  vectorize_all = FALSE
  )
 
- switch(
+ spectra <- switch(
  EXPR = file_ext,
  "mgf" = {
  readMgf(f = file) |>
  # TODO Change as soon as R 4.4.0 becomes oldrel
  # readMgfSplit(f = file) |>
- Spectra() |>
- sanitize_spectra(
- cutoff = cutoff,
- dalton = dalton,
- polarity = polarity,
- ppm = ppm
- )
+ Spectra()
  },
  "msp" = {
  readMsp(f = file) |>
- Spectra() |>
- sanitize_spectra(
- cutoff = cutoff,
- dalton = dalton,
- polarity = polarity,
- ppm = ppm
- )
+ Spectra()
  },
  # "sqlite" = {
  # CompDb(x = file) |>
@@ -72,13 +62,17 @@ import_spectra <- function(file,
  "rds" = {
  readRDS(file = file) |>
  data.frame() |>
- Spectra() |>
- sanitize_spectra(
- cutoff = cutoff,
- dalton = dalton,
- polarity = polarity,
- ppm = ppm
- )
+ Spectra()
  }
  )
+ if (sanitize) {
+ spectra <- spectra |>
+ sanitize_spectra(
+ cutoff = cutoff,
+ dalton = dalton,
+ polarity = polarity,
+ ppm = ppm
+ )
+ }
+ return(spectra)
 }

R/prepare_libraries_spectra.R

@@ -23,7 +23,6 @@ import::from(tidytable, tidytable, .into = environment())
 #' @include harmonize_spectra.R
 #' @include import_spectra.R
 #' @include parse_yaml_paths.R
-#' @include sanitize_spectra.R
 #'
 #' @param input File containing spectra
 #' @param polarity MS polarity
@@ -91,13 +90,9 @@ prepare_libraries_spectra <-
  log_debug("Importing")
  spectra <- lapply(X = input, FUN = import_spectra)
 
- log_debug("Sanitizing")
- spectra_sanitized <- lapply(X = spectra, FUN = sanitize_spectra)
- rm(spectra)
-
  log_debug("Extracting")
- spectra_extracted <- lapply(X = spectra_sanitized, FUN = extract_spectra)
- rm(spectra_sanitized)
+ spectra_extracted <- lapply(X = spectra, FUN = extract_spectra)
+ rm(spectra)
 
  log_debug("Harmonizing ...")
  log_debug("... pos")

R/sanitize_spectra.R

@@ -45,8 +45,7 @@ sanitize_spectra <-
  cutoff = 0,
  dalton = 0.01,
  polarity = NA,
- ppm = 10,
- ratio = 10000) {
+ ppm = 10) {
  log_debug("Applying sanitization of the spectra")
 
  if ("msLevel" %in% colnames(spectra@backend@spectraData)) {
@@ -74,8 +73,7 @@ sanitize_spectra <-
  ppm = ppm,
  mz = c(">=")
  ) |>
- scalePeaks() |>
- filterIntensity(intensity = c(1 / ratio, 1))
+ scalePeaks()
 
  if ("FEATURE_ID" %in% colnames(spectra@backend@spectraData)) {
  message("Combining spectra in case...")

codemeta.json

@@ -644,7 +644,7 @@
  "SystemRequirements": null
  },
  "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
- "fileSize": "3166.925KB",
+ "fileSize": "3166.651KB",
  "citation": [
  {
  "@type": "ScholarlyArticle",