Refactoring MS1 adducts (#141, #144)

taxonomicallyinformedannotation · Jul 2, 2024 · 0bd0931 · 0bd0931
1 parent 82d9cb9
commit 0bd0931
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Showing 28 changed files with 562 additions and 793 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -71,6 +71,8 @@ Collate:
     'import_spectra.R'
     'annotate_spectra.R'
     'calculate_entropy.R'
+    'parse_adduct.R'
+    'calculate_mass_from_adduct.R'
     'clean_bio.R'
     'columns_model.R'
     'clean_collapse.R'
@@ -126,7 +128,6 @@ Collate:
     'prepare_features_components.R'
     'prepare_features_edges.R'
     'prepare_features_tables.R'
-    'prepare_libraries_adducts.R'
     'prepare_libraries_rt.R'
     'select_sop_columns.R'
     'prepare_libraries_sop_closed.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -3,6 +3,7 @@
 export(annotate_masses)
 export(annotate_spectra)
 export(calculate_entropy)
+export(calculate_mass_from_adduct)
 export(clean_bio)
 export(clean_chemo)
 export(clean_collapse)
@@ -47,6 +48,7 @@ export(load_yaml_files)
 export(log_debug)
 export(log_pipe)
 export(normalize_peaks)
+export(parse_adduct)
 export(parse_cli_params)
 export(parse_yaml_params)
 export(parse_yaml_paths)
@@ -57,7 +59,6 @@ export(prepare_annotations_spectra)
 export(prepare_features_components)
 export(prepare_features_edges)
 export(prepare_features_tables)
-export(prepare_libraries_adducts)
 export(prepare_libraries_rt)
 export(prepare_libraries_sop_closed)
 export(prepare_libraries_sop_ecmdb)