Refactoring MS1 adducts (#141, #144)

taxonomicallyinformedannotation · Jul 2, 2024 · b3f8885 · b3f8885
1 parent a5a7af8
commit b3f8885
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Showing 5 changed files with 5 additions and 187 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -10,7 +10,6 @@ export(clean_collapse)
 export(cleanup_spectra)
 export(columns_model)
 export(complement_metadata_structures)
-export(create_adducts)
 export(create_components)
 export(create_dir)
 export(create_edges)

diff --git a/R/annotate_masses.R b/R/annotate_masses.R
@@ -454,7 +454,10 @@ annotate_masses <-
     if (nrow(df_addlossed_min_2) != 0) {
       message("Some adducts were unproperly detected, defaulting to (de)protonated")
       df_addlossed_min_2 <- df_addlossed_min_2 |>
-        tidytable::mutate(label = switch(ms_mode, "pos" = "[M+H]+", "neg" = "[M-H]-")) |>
+        tidytable::mutate(label = switch(ms_mode,
+          "pos" = "[M+H]+",
+          "neg" = "[M-H]-"
+        )) |>
         tidytable::rowwise() |>
         tidytable::mutate(mass = calculate_mass_from_adduct(adduct_string = label, mass = mz_1)) |>
         tidytable::ungroup()

diff --git a/R/create_adducts.R b/R/create_adducts.R
diff --git a/codemeta.json b/codemeta.json
@@ -553,7 +553,7 @@
     "SystemRequirements": null
   },
   "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
-  "fileSize": "4385.035KB",
+  "fileSize": "4378.302KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

diff --git a/man/create_adducts.Rd b/man/create_adducts.Rd