params_orf_group.yaml

knit_output_format: github_document
experiment:
  data_path: "/Users/shsingh/work/projects/2019_07_11_JUMP-CP/workspace/software/position-effect-correction/2.evalzoo/data"
  input_structure: "{data_path}/profiles.{extension}"
  extension: parquet
  external_metadata:
  add_dummy_metadata_column: TRUE
  split_by_column:
  significance_threshold: 0.05
  parallel_workers: 8
  aggregate_by:
  filter_by:
  reference_set:
    Metadata_pert_type:
      - negcon
  random_seed: 42
  background_type: ref
  shuffle: FALSE
  shuffle_bad_groups_threshold: 0.1
  shuffle_group:
  shuffle_strata:
  shuffle_exclude:
  subsample_fraction: 1
  subsample_pert_strata:
    - Metadata_Plate
  subsample_reference_strata:
    - Metadata_Well
  similarity_method: cosine
  sim_params:
    drop_group:
      Metadata_pert_type:
        - poscon
    reference:
        Metadata_reference_or_other:
          reference
    all_same_cols_ref:
      - Metadata_dummy
    all_same_cols_rep:
      - Metadata_JCP2022
      - Metadata_reference_or_other
    all_same_cols_rep_ref:
    any_different_cols_non_rep:
    all_same_cols_non_rep:
    all_different_cols_non_rep:
    all_same_cols_group:
      - Metadata_Well
    any_different_cols_group:
      - Metadata_JCP2022
    annotation_cols:
      - Metadata_JCP2022
      - Metadata_Well
      - Metadata_reference_or_other