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yeast_comparative_analysis

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genomics
transcription-factors
yeast
saccharomyces-cerevisiae
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cmatkhan commited on
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1 Parent(s): 0381f94

updating dto

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Files changed (33) hide show
  1. README.md +7 -0
  2. dto/binding_repo_dataset=callingcards-annotated_features/perturbation_repo_dataset=hackett_2020-hackett_2020/part-0.parquet +2 -2
  3. dto/binding_repo_dataset=callingcards-annotated_features/perturbation_repo_dataset=hu_2007_reimand_2010-hu_2007_reimand_2010/part-0.parquet +2 -2
  4. dto/binding_repo_dataset=callingcards-annotated_features/perturbation_repo_dataset=hughes_2006-knockout/part-0.parquet +2 -2
  5. dto/binding_repo_dataset=callingcards-annotated_features/perturbation_repo_dataset=hughes_2006-overexpression/part-0.parquet +2 -2
  6. dto/binding_repo_dataset=callingcards-annotated_features/perturbation_repo_dataset=kemmeren_2014-kemmeren_2014/part-0.parquet +2 -2
  7. dto/binding_repo_dataset=callingcards-annotated_features/perturbation_repo_dataset=mahendrawada_2025-rnaseq_reprocessed/part-0.parquet +2 -2
  8. dto/binding_repo_dataset=callingcards-annotated_features_combined/perturbation_repo_dataset=hackett_2020-hackett_2020/part-0.parquet +2 -2
  9. dto/binding_repo_dataset=callingcards-annotated_features_combined/perturbation_repo_dataset=hu_2007_reimand_2010-hu_2007_reimand_2010/part-0.parquet +2 -2
  10. dto/binding_repo_dataset=callingcards-annotated_features_combined/perturbation_repo_dataset=hughes_2006-knockout/part-0.parquet +2 -2
  11. dto/binding_repo_dataset=callingcards-annotated_features_combined/perturbation_repo_dataset=hughes_2006-overexpression/part-0.parquet +2 -2
  12. dto/binding_repo_dataset=callingcards-annotated_features_combined/perturbation_repo_dataset=kemmeren_2014-kemmeren_2014/part-0.parquet +2 -2
  13. dto/binding_repo_dataset=callingcards-annotated_features_combined/perturbation_repo_dataset=mahendrawada_2025-rnaseq_reprocessed/part-0.parquet +2 -2
  14. dto/binding_repo_dataset=harbison_2004-harbison_2004/perturbation_repo_dataset=hackett_2020-hackett_2020/part-0.parquet +2 -2
  15. dto/binding_repo_dataset=harbison_2004-harbison_2004/perturbation_repo_dataset=hu_2007_reimand_2010-hu_2007_reimand_2010/part-0.parquet +2 -2
  16. dto/binding_repo_dataset=harbison_2004-harbison_2004/perturbation_repo_dataset=hughes_2006-knockout/part-0.parquet +2 -2
  17. dto/binding_repo_dataset=harbison_2004-harbison_2004/perturbation_repo_dataset=hughes_2006-overexpression/part-0.parquet +2 -2
  18. dto/binding_repo_dataset=harbison_2004-harbison_2004/perturbation_repo_dataset=kemmeren_2014-kemmeren_2014/part-0.parquet +2 -2
  19. dto/binding_repo_dataset=harbison_2004-harbison_2004/perturbation_repo_dataset=mahendrawada_2025-rnaseq_reprocessed/part-0.parquet +2 -2
  20. dto/binding_repo_dataset=mahendrawada_2025-chec_mahendrawada_m2025_af_combined/perturbation_repo_dataset=hackett_2020-hackett_2020/part-0.parquet +2 -2
  21. dto/binding_repo_dataset=mahendrawada_2025-chec_mahendrawada_m2025_af_combined/perturbation_repo_dataset=hu_2007_reimand_2010-hu_2007_reimand_2010/part-0.parquet +2 -2
  22. dto/binding_repo_dataset=mahendrawada_2025-chec_mahendrawada_m2025_af_combined/perturbation_repo_dataset=hughes_2006-knockout/part-0.parquet +2 -2
  23. dto/binding_repo_dataset=mahendrawada_2025-chec_mahendrawada_m2025_af_combined/perturbation_repo_dataset=hughes_2006-overexpression/part-0.parquet +2 -2
  24. dto/binding_repo_dataset=mahendrawada_2025-chec_mahendrawada_m2025_af_combined/perturbation_repo_dataset=kemmeren_2014-kemmeren_2014/part-0.parquet +2 -2
  25. dto/binding_repo_dataset=mahendrawada_2025-chec_mahendrawada_m2025_af_combined/perturbation_repo_dataset=mahendrawada_2025-rnaseq_reprocessed/part-0.parquet +2 -2
  26. dto/binding_repo_dataset=rossi_2021-rossi_2021_af_combined/perturbation_repo_dataset=hackett_2020-hackett_2020/part-0.parquet +2 -2
  27. dto/binding_repo_dataset=rossi_2021-rossi_2021_af_combined/perturbation_repo_dataset=hu_2007_reimand_2010-hu_2007_reimand_2010/part-0.parquet +2 -2
  28. dto/binding_repo_dataset=rossi_2021-rossi_2021_af_combined/perturbation_repo_dataset=hughes_2006-knockout/part-0.parquet +2 -2
  29. dto/binding_repo_dataset=rossi_2021-rossi_2021_af_combined/perturbation_repo_dataset=hughes_2006-overexpression/part-0.parquet +2 -2
  30. dto/binding_repo_dataset=rossi_2021-rossi_2021_af_combined/perturbation_repo_dataset=kemmeren_2014-kemmeren_2014/part-0.parquet +2 -2
  31. dto/binding_repo_dataset=rossi_2021-rossi_2021_af_combined/perturbation_repo_dataset=mahendrawada_2025-rnaseq_reprocessed/part-0.parquet +2 -2
  32. scripts/dto_preparation.R +8 -9
  33. scripts/parse_dto_results.R +1 -0
README.md CHANGED
@@ -38,6 +38,13 @@ configs:
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  'repo_id;config_name;sample_id' (e.g.,
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  'BrentLab/Hackett_2020;hackett_2020;200')
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  role: source_sample
 
 
 
 
 
 
 
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  - name: binding_rank_threshold
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  dtype: float64
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  description: >-
 
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  'repo_id;config_name;sample_id' (e.g.,
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  'BrentLab/Hackett_2020;hackett_2020;200')
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  role: source_sample
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+ - name: pr_ranking_column
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+ dtype:
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+ class_label: ["log2fc", "pvalue"]
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+ description: >-
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+ Describes which column, effect (log2fc) or pvalue was used
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+ in ranking the perturbation response data. see scripts/dto_preparation.R
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+ for more info on each dataset
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  - name: binding_rank_threshold
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  dtype: float64
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  description: >-
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scripts/dto_preparation.R CHANGED
@@ -286,7 +286,6 @@ all_pr_dtos = list(
286
  )
287
  )
288
 
289
- # Write out DTO ranked lists
290
  # Write out DTO ranked lists
291
  write_out_pr_dto_lists = function(pr_dataset_name,
292
  binding_pr_set_name,
@@ -431,11 +430,11 @@ create_pr_lookups = function(pr_dataset_name, binding_pr_set_name,
431
  # }
432
 
433
  # Summary of incomplete cases across all datasets
434
- incomplete_summary = map_dfr(names(lookup_results), ~{
435
- map_dfr(names(lookup_results[[.x]]), function(binding_name) {
436
- lookup_results[[.x]][[binding_name]]$incomplete_after_filtering %>%
437
- mutate(pr_dataset = .x, binding_dataset = binding_name)
438
- })
439
- })
440
-
441
- print(incomplete_summary %>% count(pr_dataset, binding_dataset, missing_type))
 
286
  )
287
  )
288
 
 
289
  # Write out DTO ranked lists
290
  write_out_pr_dto_lists = function(pr_dataset_name,
291
  binding_pr_set_name,
 
430
  # }
431
 
432
  # Summary of incomplete cases across all datasets
433
+ # incomplete_summary = map_dfr(names(lookup_results), ~{
434
+ # map_dfr(names(lookup_results[[.x]]), function(binding_name) {
435
+ # lookup_results[[.x]][[binding_name]]$incomplete_after_filtering %>%
436
+ # mutate(pr_dataset = .x, binding_dataset = binding_name)
437
+ # })
438
+ # })
439
+
440
+ # print(incomplete_summary %>% count(pr_dataset, binding_dataset, missing_type))
scripts/parse_dto_results.R CHANGED
@@ -123,6 +123,7 @@ hf_results_df = dto_results_df %>%
123
  binding_rank_threshold, perturbation_rank_threshold,
124
  binding_set_size, perturbation_set_size,
125
  dto_fdr, dto_empirical_pvalue,
 
126
  binding_repo_dataset, perturbation_repo_dataset)
127
 
128
 
 
123
  binding_rank_threshold, perturbation_rank_threshold,
124
  binding_set_size, perturbation_set_size,
125
  dto_fdr, dto_empirical_pvalue,
126
+ pr_ranking_column,
127
  binding_repo_dataset, perturbation_repo_dataset)
128
 
129