more tidytable

R/clean_bio.R

@@ -561,6 +561,7 @@ clean_bio <-
       ) |>
       # In case there are no consensus at all because no network
       tidytable::mutate(tidytable::across(tidytable::where(is.logical), as.character)) |>
+      data.frame() |>
       tidytable::tidytable()
 
     # TODO Think about better scoring option

R/harmonize_spectra.R

@@ -137,6 +137,7 @@ harmonize_spectra <- function(spectra,
 
   spectra_harmonized <- spectra_filtered |>
     tidytable::full_join(spectra_missing) |>
+    data.frame() |>
     tidytable::tidytable() |>
     tidytable::select(
       collision_energy,

R/prepare_libraries_sop_closed.R

@@ -53,6 +53,7 @@ prepare_libraries_sop_closed <-
         tidytable::fread(
           na.strings = c("", "NA")
         ) |>
+        data.frame() |>
         tidytable::tidytable()
 
       log_debug(x = "Formatting closed resource")

R/prepare_libraries_sop_ecmdb.R

@@ -46,6 +46,7 @@ prepare_libraries_sop_ecmdb <-
           description = input,
           filename = file
         )) |>
+          data.frame() |>
           tidytable::tidytable()
       })
 

R/prepare_libraries_sop_merged.R

@@ -136,7 +136,8 @@ prepare_libraries_sop_merged <-
     }
 
     tables <- tidytable::bind_rows(libraries) |>
-      tidytable::data.table() |>
+      data.frame() |>
+      tidytable::tidytable() |>
       split_tables_sop()
 
     log_debug(x = "Keeping keys")

R/weight_bio.R

@@ -775,6 +775,7 @@ weight_bio <-
         score_pondered_bio
       ) |>
       tidytable::arrange(as.numeric(feature_id)) |>
+      data.frame() |>
       tidytable::tidytable()
 
     return(biologically_weighted_full)