updating mindel data

scripts/parse_dto_results.R

@@ -69,57 +69,55 @@ dto_results_list = future_imap(dto_results_lookup$result_file, ~{
 
 dto_results_df = bind_cols(dto_results_lookup, bind_rows(dto_results_list))
 
-# hf_results_df = dto_results_df %>%
-#     mutate(
-#         binding_id = case_when(
-#             binding_source == "cc"
-#             ~ paste0("BrentLab/callingcards;annotated_feature_reprocess_mindel;",
-#                      binding_id),
-#             binding_source == "chipexo"
-#             ~ paste0("BrentLab/rossi_2021;rossi_2021_af_combined_mindel;",
-#                      binding_id),
-#             binding_source == "mahendrawada_chec"
-#             ~ paste0("BrentLab/mahendrawada_2025;chec_mahendrawada_m2025_af_combined_mindel;",
-#                      binding_id)),
-#         perturbation_id = case_when(
-#             pr_source == "hackett" ~ paste0("BrentLab/hackett_2020;hackett_2020;", perturbation_id),
-#             pr_source == "hughes_oe" ~ paste0("BrentLab/hughes_2006;overexpression;", perturbation_id),
-#             pr_source == "hughes_ko" ~ paste0("BrentLab/hughes_2006;knockout;", perturbation_id),
-#             pr_source == "hu_reimand" ~ paste0("BrentLab/hu_2007_reimand_2010;hu_2007_reimand_2010;", perturbation_id),
-#             pr_source == "kemmeren" ~ paste0("BrentLab/kemmeren_2014;kemmeren_2014;", perturbation_id),
-#             pr_source == "mahendrawada_rnaseq" ~ paste0("BrentLab/mahendrawada_2025;rnaseq_reprocessed;", perturbation_id),
-#             .default = "ERROR"),
-#         binding_repo_dataset = case_when(
-#             binding_source == "cc" & str_detect(binding_id, "-")
-#             ~ "callingcards-annotated_features_combined",
-#             binding_source == "cc" & str_detect(binding_id, "-", negate=TRUE)
-#             ~ "callingcards-annotated_features",
-#             binding_source == "chipexo"
-#             ~ "rossi_2021-rossi_2021_af_combined",
-#             binding_source == "harbison"
-#             ~ paste0("harbison_2004-harbison_2004"),
-#             binding_source == "mahendrawada_chec"
-#             ~ "mahendrawada_2025-chec_mahendrawada_m2025_af_combined"),
-#         perturbation_repo_dataset = case_when(
-#             pr_source == "hackett" ~ paste0("hackett_2020-hackett_2020"),
-#             pr_source == "hughes_oe" ~ paste0("hughes_2006-overexpression"),
-#             pr_source == "hughes_ko" ~ paste0("hughes_2006-knockout"),
-#             pr_source == "hu_reimand" ~ paste0("hu_2007_reimand_2010-hu_2007_reimand_2010"),
-#             pr_source == "kemmeren" ~ paste0("kemmeren_2014-kemmeren_2014"),
-#             pr_source == "mahendrawada_rnaseq" ~ paste0("mahendrawada_2025-rnaseq_reprocessed"),
-#             .default = "ERROR")) %>%
-#     dplyr::rename(binding_rank_threshold = rank1,
-#                   perturbation_rank_threshold = rank2,
-#                   binding_set_size = set1_len,
-#                   perturbation_set_size = set2_len,
-#                   dto_fdr = fdr,
-#                   dto_empirical_pvalue = empirical_pvalue) %>%
-#     select(binding_id, perturbation_id,
-#            binding_rank_threshold, perturbation_rank_threshold,
-#            binding_set_size, perturbation_set_size,
-#            dto_fdr, dto_empirical_pvalue,
-#            pr_ranking_column,
-#            binding_repo_dataset, perturbation_repo_dataset)
+hf_results_df = dto_results_df %>%
+    mutate(
+        binding_id = case_when(
+            binding_source == "cc"
+            ~ paste0("BrentLab/callingcards;annotated_feature_reprocess_mindel;",
+                     binding_id),
+            binding_source == "chipexo"
+            ~ paste0("BrentLab/rossi_2021;rossi_2021_af_combined_mindel;",
+                     binding_id),
+            binding_source == "mahendrawada_chec"
+            ~ paste0("BrentLab/mahendrawada_2025;chec_mahendrawada_m2025_af_combined_mindel;",
+                     binding_id)),
+        perturbation_id = case_when(
+            pr_source == "hackett" ~ paste0("BrentLab/hackett_2020;hackett_2020;", perturbation_id),
+            pr_source == "hughes_oe" ~ paste0("BrentLab/hughes_2006;overexpression;", perturbation_id),
+            pr_source == "hughes_ko" ~ paste0("BrentLab/hughes_2006;knockout;", perturbation_id),
+            pr_source == "hu_reimand" ~ paste0("BrentLab/hu_2007_reimand_2010;hu_2007_reimand_2010;", perturbation_id),
+            pr_source == "kemmeren" ~ paste0("BrentLab/kemmeren_2014;kemmeren_2014;", perturbation_id),
+            pr_source == "mahendrawada_rnaseq" ~ paste0("BrentLab/mahendrawada_2025;rnaseq_reprocessed;", perturbation_id),
+            .default = "ERROR"),
+        binding_repo_dataset = case_when(
+            binding_source == "cc"
+            ~ "callingcards-annotated_feature_reprocess_mindel",
+            binding_source == "chipexo"
+            ~ "rossi_2021-rossi_2021_af_combined_mindel",
+            binding_source == "harbison"
+            ~ paste0("harbison_2004-harbison_2004"),
+            binding_source == "mahendrawada_chec"
+            ~ "mahendrawada_2025-chec_mahendrawada_m2025_af_combined_mindel"),
+        perturbation_repo_dataset = case_when(
+            pr_source == "hackett" ~ paste0("hackett_2020-hackett_2020"),
+            pr_source == "hughes_oe" ~ paste0("hughes_2006-overexpression"),
+            pr_source == "hughes_ko" ~ paste0("hughes_2006-knockout"),
+            pr_source == "hu_reimand" ~ paste0("hu_2007_reimand_2010-hu_2007_reimand_2010"),
+            pr_source == "kemmeren" ~ paste0("kemmeren_2014-kemmeren_2014"),
+            pr_source == "mahendrawada_rnaseq" ~ paste0("mahendrawada_2025-rnaseq_reprocessed"),
+            .default = "ERROR")) %>%
+    dplyr::rename(binding_rank_threshold = rank1,
+                  perturbation_rank_threshold = rank2,
+                  binding_set_size = set1_len,
+                  perturbation_set_size = set2_len,
+                  dto_fdr = fdr,
+                  dto_empirical_pvalue = empirical_pvalue) %>%
+    select(binding_id, perturbation_id,
+           binding_rank_threshold, perturbation_rank_threshold,
+           binding_set_size, perturbation_set_size,
+           dto_fdr, dto_empirical_pvalue,
+           pr_ranking_column,
+           binding_repo_dataset, perturbation_repo_dataset)
 
 # arrow::write_dataset(
 #     hf_results_df,