8  Genetic enrichment

module_genetic_enrichment/targets.R filters enabled human aggregations, resolves one configured Open Targets study set per aggregation, and attaches symbols for WNN metadata, graphs, embeddings, consensus peaks, chromVAR state, and ATAC fragments.

The main target fragments live in setup_targets.R, gchromVAR_targets.R, SCAVENGE_graph_targets.R, SCAVENGE_group_targets.R, GWAS_chromVAR_cell_type_targets.R, and GWAS_chromVAR_contribution_targets.R. The user-facing release, method-selection, and interpretation contracts are documented in Genetic enrichment.

8.1 Single-nucleus and graph-based enrichment

This view covers the configured GWAS inputs, single-nucleus enrichment state, graph propagation, and downstream trait summaries. Additional cell-type contribution and locus-attribution branches may be pruned from this compact orientation view; use the manifest for the complete graph.

The sparse SCAVENGE reimplementation, deliberate graph and permutation differences, and validation evidence are recorded in Algorithmic implementations, deviations and validation.

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}}%%
%%{init: {'flowchart': {'defaultRenderer': 'elk'}}}%%
flowchart TB
  chromVAR_peak_expectation.ATAC.immune_human_2x(["chromVAR_peak_expectation.ATAC.<aggregation_name>"]):::none --> chromVAR_background_bins.ATAC.immune_human_2x(["chromVAR_background_bins.ATAC.<aggregation_name>"]):::none
  chromVAR_obj.ATAC.immune_human_2x(["chromVAR_obj.ATAC.<aggregation_name>"]):::none --> chromVAR_background_bins.ATAC.immune_human_2x(["chromVAR_background_bins.ATAC.<aggregation_name>"]):::none
  chromVAR_obj.ATAC.immune_human_2x(["chromVAR_obj.ATAC.<aggregation_name>"]):::none --> chromVAR_peak_expectation.ATAC.immune_human_2x(["chromVAR_peak_expectation.ATAC.<aggregation_name>"]):::none
  chromVAR_z_score_records.single_nucleus.genetic_enrichment.immune_human_2x["chromVAR_z_score_records.single_nucleus.<module_name>.<aggregation_name>"]:::none --> SCAVENGE_result_records.LSI_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x["SCAVENGE_result_records.LSI_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]:::none
  graph_matrix.LSI_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x(["graph_matrix.LSI_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]):::none --> SCAVENGE_result_records.LSI_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x["SCAVENGE_result_records.LSI_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]:::none
  graph_matrix.PCA_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x(["graph_matrix.PCA_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]):::none --> SCAVENGE_result_records.PCA_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x["SCAVENGE_result_records.PCA_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]:::none
  chromVAR_z_score_records.single_nucleus.genetic_enrichment.immune_human_2x["chromVAR_z_score_records.single_nucleus.<module_name>.<aggregation_name>"]:::none --> SCAVENGE_result_records.PCA_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x["SCAVENGE_result_records.PCA_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]:::none
  chromVAR_z_score_records.single_nucleus.genetic_enrichment.immune_human_2x["chromVAR_z_score_records.single_nucleus.<module_name>.<aggregation_name>"]:::none --> SCAVENGE_result_records.WNN_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x["SCAVENGE_result_records.WNN_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]:::none
  graph_matrix.WNN_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x(["graph_matrix.WNN_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]):::none --> SCAVENGE_result_records.WNN_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x["SCAVENGE_result_records.WNN_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]:::none
  chromVAR_obj.ATAC.immune_human_2x(["chromVAR_obj.ATAC.<aggregation_name>"]):::none --> chromVAR_z_score_records.single_nucleus.genetic_enrichment.immune_human_2x["chromVAR_z_score_records.single_nucleus.<module_name>.<aggregation_name>"]:::none
  chromVAR_background_bins.ATAC.immune_human_2x(["chromVAR_background_bins.ATAC.<aggregation_name>"]):::none --> chromVAR_z_score_records.single_nucleus.genetic_enrichment.immune_human_2x["chromVAR_z_score_records.single_nucleus.<module_name>.<aggregation_name>"]:::none
  chromVAR_peak_expectation.ATAC.immune_human_2x(["chromVAR_peak_expectation.ATAC.<aggregation_name>"]):::none --> chromVAR_z_score_records.single_nucleus.genetic_enrichment.immune_human_2x["chromVAR_z_score_records.single_nucleus.<module_name>.<aggregation_name>"]:::none
  GWAS_peak_weight_records.genetic_enrichment.immune_human_2x["GWAS_peak_weight_records.<module_name>.<aggregation_name>"]:::none --> chromVAR_z_score_records.single_nucleus.genetic_enrichment.immune_human_2x["chromVAR_z_score_records.single_nucleus.<module_name>.<aggregation_name>"]:::none
  chromVAR_obj.ATAC.immune_human_2x(["chromVAR_obj.ATAC.<aggregation_name>"]):::none --> GWAS_peak_weight_records.genetic_enrichment.immune_human_2x["GWAS_peak_weight_records.<module_name>.<aggregation_name>"]:::none
  open_targets_credible_set_dataset_path(["open_targets_credible_set_dataset_path"]):::none --> GWAS_inputs_tibble.genetic_enrichment.immune_human_2x(["GWAS_inputs_tibble.<module_name>.<aggregation_name>"]):::none
  open_targets_credible_set_dataset_path(["open_targets_credible_set_dataset_path"]):::none --> GWAS_peak_weight_records.genetic_enrichment.immune_human_2x["GWAS_peak_weight_records.<module_name>.<aggregation_name>"]:::none
  SCAVENGE_result_records.LSI_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x["SCAVENGE_result_records.LSI_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]:::none --> TRS_summary_tibble.LSI_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x(["TRS_summary_tibble.LSI_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]):::none
  SCAVENGE_result_records.PCA_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x["SCAVENGE_result_records.PCA_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]:::none --> TRS_summary_tibble.PCA_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x(["TRS_summary_tibble.PCA_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]):::none
  SCAVENGE_result_records.WNN_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x["SCAVENGE_result_records.WNN_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]:::none --> TRS_summary_tibble.WNN_harmony_SNN.SCAVENGE.single_nucleus.genetic_enrichment.immune_human_2x(["TRS_summary_tibble.WNN_harmony_SNN.SCAVENGE.single_nucleus.<module_name>.<aggregation_name>"]):::none