benchmark update

taxonomicallyinformedannotation · Jul 23, 2023 · 00ad552 · 00ad552
1 parent bbacd8a
commit 00ad552
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Showing 3 changed files with 233 additions and 105 deletions.
diff --git a/R/sanitize_spectra_benchmark.R b/R/sanitize_spectra_benchmark.R
@@ -28,8 +28,6 @@ sanitize_spectra_benchmark <-
  meta_neg_path = "data/interim/benchmark/benchmark_meta_neg.tsv") {
  sp$precursorMz <- as.numeric(sp$PRECURSOR_MZ)
  sp$precursorCharge <- as.integer(sp$CHARGE)
- sp$acquisitionNum <- as.integer(sp$SCANS)
- sp$scanIndex <- as.integer(sp$SCANS)
 
  sp_clean <- sp |>
  Spectra::addProcessing(remove_above_precursor(),
@@ -114,8 +112,8 @@ sanitize_spectra_benchmark <-
  sp_neg <- sp_clean[sp_clean$SPECTRUMID %in% df_clean_neg$ccmslib]
  sp_pos$feature_id <- df_clean_pos$feature_id
  sp_neg$feature_id <- df_clean_neg$feature_id
- sp_pos$SCANS <- df_clean_pos$feature_id
- sp_neg$SCANS <- df_clean_neg$feature_id
+ sp_pos$spectrum_id <- df_clean_pos$feature_id
+ sp_neg$spectrum_id <- df_clean_neg$feature_id
 
  spectra_harmonized_pos <- sp_pos |>
  extract_spectra() |>
@@ -134,7 +132,7 @@ sanitize_spectra_benchmark <-
  col_po = "polarity",
  col_sm = "smiles",
  col_sn = NA,
- col_si = "SPECTRUMID",
+ col_si = "spectrum_id",
  col_sp = NA,
  col_sy = NA,
  col_xl = NA,
@@ -158,13 +156,20 @@ sanitize_spectra_benchmark <-
  col_po = "polarity",
  col_sm = "smiles",
  col_sn = NA,
- col_si = "SPECTRUMID",
+ col_si = "spectrum_id",
  col_sp = NA,
  col_sy = NA,
  col_xl = NA,
  mode = "neg"
  )
 
+ spectra_harmonized_pos$acquisitionNum <-
+ spectra_harmonized_pos$spectrum_id |>
+ as.integer()
+ spectra_harmonized_neg$acquisitionNum <-
+ spectra_harmonized_neg$spectrum_id |>
+ as.integer()
+
  log_debug("Exporting")
  spectra_harmonized_pos |>
  Spectra::Spectra() |>

diff --git a/R/taxize_spectra_benchmark.R b/R/taxize_spectra_benchmark.R
@@ -53,8 +53,16 @@ taxize_spectra_benchmark <-
  )) |>
  tidytable::select(
  feature_id,
- contains("organism_taxonomy_"),
- -contains("ott")
+ sample_organism_01_domain = organism_taxonomy_01domain,
+ sample_organism_02_kingdom = organism_taxonomy_02kingdom,
+ sample_organism_03_phylum = organism_taxonomy_03phylum,
+ sample_organism_04_class = organism_taxonomy_04class,
+ sample_organism_05_order = organism_taxonomy_05order,
+ sample_organism_06_family = organism_taxonomy_06family,
+ sample_organism_07_tribe = organism_taxonomy_07tribe,
+ sample_organism_08_genus = organism_taxonomy_08genus,
+ sample_organism_09_species = organism_taxonomy_09species,
+ sample_organism_10_varietas = organism_taxonomy_10varietas
  )
 
  export_output(x = features_taxed, file = output)