Adding SIRIUS feature tables support (#185)

NEWS.md

@@ -1,5 +1,9 @@
 # tima
 
+# tima 2.11.1
+
+* Added `SIRIUS` feature tables support (#185)
+
 # tima 2.11.0
 
 * Added convenience function to change small parameters (#177)

R/change_params_small.R

@@ -8,7 +8,7 @@
 #' @include load_yaml_files.R
 #'
 #' @param fil_pat The pattern identifying your whole job. You can put whatever you want. STRING
-#' @param fil_fea_raw The path to the file containing your features' intensities. Can be generated by mzmine3 or SLAW. STRING
+#' @param fil_fea_raw The path to the file containing your features' intensities. Can be generated by mzmine, SLAW, or SIRIUS. STRING
 #' @param fil_met_raw The path to the file containing your metadata. If your experiment contains a single taxon, you can provide it below instead. STRING
 #' @param fil_sir_raw The directory containing the sirius annotations. STRING
 #' @param fil_spe_raw The path to the file containing your features' spectra. Can contain MS1 and/or MS2 spectra. STRING

R/prepare_taxa.R

@@ -100,12 +100,15 @@ prepare_taxa <-
     log_debug(x = "... requires 'Peak area' or ':area'
               in columns (mzmine format)")
     log_debug(x = "... or 'quant_' in columns (SLAW format)")
+    log_debug(x = "... or 'Peak height' in columns (SIRIUS format)")
+
     feature_table <- feature_table_0 |>
       tidytable::select(
         tidyselect::all_of(c(name_features)),
         tidyselect::matches(" Peak area"),
         tidyselect::matches(":area"),
-        tidyselect::matches("quant_")
+        tidyselect::matches("quant_"),
+        tidyselect::matches(" Peak height")
       ) |>
       tidytable::select(-tidyselect::matches("quant_peaktable")) |>
       tidyfst::col_rn(var = name_features)
@@ -132,6 +135,12 @@ prepare_taxa <-
         replacement = "",
         vectorize_all = FALSE
       )
+    colnames(feature_table) <- colnames(feature_table) |>
+      stringi::stri_replace_all_fixed(
+        pattern = " Peak height",
+        replacement = "",
+        vectorize_all = FALSE
+      )
     log_debug(x = "... filtering top K intensities per feature")
     top_n <- feature_table |>
       tidyfst::rn_col() |>

inst/params/prepare_params.yaml

@@ -4,7 +4,7 @@ files:
   pattern: example
   features:
     #' The path to the file containing your features' intensities.
-    #' Can be generated by mzmine3 or SLAW. STRING
+    #' Can be generated by mzmine, SLAW, or SIRIUS. STRING
     raw: data/source/example_features.csv
   metadata:
     #' The path to the file containing your metadata.