Use susie_ser for sumstat PIP screening#498
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Final Report 1. Interface Separation Rationale: Direct ColocBoost users and xQTL protocol users need different entrypoints. Mixing both workflows in one function made the API confusing and encouraged duplicated QC logic. Key changes: - Added/standardized colocboost_analysis() as the direct user-facing wrapper. - Accepts the same core inputs as colocboost() through .... - Adds optional QC/imputation parameters. - If no QC is requested, it behaves as a minimal call-through to colocboost(). - If QC is requested, it prepares cleaned inputs first, then calls colocboost(). - Added/standardized colocboost_pipeline() as the protocol-oriented wrapper. - Starts from region_data produced by load_multitask_regional_data(). - Designed for xQTL-protocol workflows. - Runs QC once, then reuses cleaned inputs across xQTL-only, joint-GWAS, and separate-GWAS analyses. 2. RegionalData Conversion Layer Rationale: Loaded regional data should be converted into reusable analysis inputs without reloading files or duplicating conversion logic. Key changes: - Added reusable adapters: - region_data_to_rss_input() for summary-stat/RSS workflows. - region_data_to_ind_input() for individual-level workflows. - region_data_to_colocboost_input() for ColocBoost-specific assembly. - Preserved shared heavy objects such as X, LD, and X_ref. - Used dictionaries such as dict_YX and dict_sumstatLD to avoid duplicated matrix storage. 3. Shared QC Refactor Rationale: QC logic should be reusable across ColocBoost, SuSiE RSS, and individual-level SuSiE workflows instead of being embedded separately in each pipeline. Key changes: - Added qc_individual_data() for individual-level QC. - Expanded summary_stats_qc() to support combined RSS/ColocBoost summary-stat QC while preserving its historical LD-mismatch QC behavior. - Clarified qc_method behavior: - NULL, "none", and "rss_qc" mean basic summary-stat harmonization only. - "slalom" and "dentist" add optional LD-mismatch outlier QC. - Added QC progress messages for stage tracking, retained counts, skips, and warnings. 4. X_ref-Based Imputation Rationale: When genotype reference X_ref is available, imputation should use the genotype reference directly rather than deriving LD blocks, because LD block partitioning can alter imputation behavior. Key changes: - Final behavior uses whole-region scaled X_ref with RAISS genotype/SVD imputation. - The temporary scaled matrix is used only inside imputation. - The original X_ref remains the reference passed into the final colocboost() call. - The implementation avoids full LD construction for X_ref imputation. - Added tests showing: - raw X_ref SVD can differ from LD-based RAISS; - scaled X_ref SVD matches LD scale in a controlled single-matrix case; - colocboost_analysis(..., X_ref=..., impute=TRUE) uses scaled genotype/SVD and does not call compute_LD(). Important report observation: - Old LD-block RAISS retained fewer variants for ENSG00000155304: 166 -> 7 and 167 -> 7. - Whole-region scaled X_ref SVD retained more: 166 -> 16 and 167 -> 13. - This difference is expected and should be highlighted as evidence that LD block partitioning changes imputation behavior. 5. Protocol Compatibility and Minimal Loader Fixes Rationale: The implementation should support the uploaded chr21 test data and xQTL-protocol use case while keeping loader changes minimal. Key changes: - Kept all changes within pecotmr; no changes were made to the core colocboost() function. - Made only minimal loader-related fixes required by smoke testing: - multi-genotype-source loading via match_geno_pheno; - header handling for tabix-backed summary-stat files; - whitespace-padded covariate numeric parsing. - Updated protocol-facing naming to use colocboost_pipeline(). 6. Documentation and Tests Rationale: The new interfaces, QC behavior, and imputation decision need clear user-facing documentation and regression coverage so future changes do not reintroduce ambiguity. Key changes: - Updated documentation/man pages and vignette references for the new ColocBoost interfaces. - Added chr21 smoke-test deliverable notes emphasizing the X_ref imputation decision. - Added focused regression tests for: - colocboost_analysis() direct-input behavior; - colocboost_pipeline() protocol-level behavior; - reusable summary-stat QC behavior; - RAISS raw/scaled genotype-reference behavior; - X_ref-backed imputation avoiding compute_LD(). - Focused tests passed: - test_raiss.R - test_sumstats_qc.R - test_colocboost_pipeline.R - Chr21 smoke tests completed on two genes across six scenarios, covering no-AD xQTL-only, basic QC, imputation, PIP screening, SLALOM QC, and combined modes.
Remove the legacy rss_qc alias so summary_stats_qc only accepts none, slalom, and dentist.
# Conflicts: # NAMESPACE # R/sumstats_qc.R # R/univariate_pipeline.R # man/summary_stats_qc.Rd # tests/testthat/test_sumstats_qc.R
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two minor changes