sigmutselcovs covariate matrices: TCGA-DLBC

Pre-built per-gene covariate matrices for TCGA-DLBC (Diffuse large B-cell lymphoma. GTEx maps to Whole_Blood/Spleen (no lymph-node column in GTEx). No TCGA ATAC-seq coverage (atac: null). Roadmap uses E032 (primary B cells from peripheral blood, the direct cell-of-origin match, 6/7 marks -- H3K9ac 404s) plus E062 (primary PBMCs, broader immune mix, 7/7 marks) for fuller coverage, same two-epigenome pattern as CHOL/CESC. Repliseq uses GM12878 (EBV-transformed lymphoblastoid B-cell line), the standard ENCODE UW 6-fraction Repli-seq series, hg19, all 6 fractions live-verified -- the closest available cell-type match for a B-cell malignancy, analogous to CHOL's HepG2/BRCA's MCF-7 choices. encode_chromatin added 2026-09-03 (expanded-covariate-sources task, Objective A.3): DNase-seq substituted for the missing TCGA ATAC-seq coverage, same rationale as OV -- adult primary peripheral-blood B cell DNase-seq exists natively on ENCODE (8 released adult experiments; one used here), matching E032's cell-of-origin choice. encode_chromatin cell lines added 2026-09-07: Karpas-422, OCI-LY1, OCI-LY3, OCI-LY7 and SU-DHL-6 are actual diffuse large B-cell lymphoma cell lines (not just blood/lymphoid-adjacent like GM12878/E032/E062 above) -- the closest cell-type match this registry has found for any cohort, found via Martincorena et al. 2017's STAR Methods confirming dNdScv's own matrix is cell-line-based, which prompted checking ENCODE's classification=cell+line facet for a disease-matched line here.), built with sigmutselcovs: GTEx tissue-matched gene expression, TCGA per-sample gene expression, replication timing (mean replication time and CLR-transformed S-phase fractions), Roadmap Epigenomics histone marks, and TCGA ATAC-seq accessibility, indexed by Ensembl gene ID. Files: cov_matrix_full.parquet — the full matrix (all covariate columns) cov_matrix_pca.parquet — PCA-reduced to 901 components, the smallest number reaching 99% cumulative explained variance (see pca_manifest.json) cov_matrix_columns.csv — a data dictionary: one row per column of the full matrix, with source, description, assembly, and units build_manifest.json, pca_manifest.json — build provenance and PCA parameters Full source citations and methodology: SOURCES.md. Release of 2026-10-26. Every chromatin and ATAC column is one track, summarized as log1p of the mean signal over the gene's CDS span (first to last coding base); replication timing covers chrX. cov_matrix_pca.parquet now reduces the combined matrix: this cohort's own covariates plus the tissue-agnostic GENERIC pool (GENERIC record), with the pool's columns for chromatin tracks this cohort already has left out. That is the matrix the sigmutsel covariate model is fitted on; it predicts held-out mutation counts better than the cohort's own matrix alone in the cohorts tested, so the first components of this artifact are the ones a model should use. Versions before 2026-10-26 reduced the own matrix alone. cov_matrix_full.parquet is still the cohort's own matrix; GENERIC's is in its record. pca_manifest.json records which matrix was reduced (matrix) and the column counts. To rebuild: sigmutselcovs pca-artifact DLBC --data-dir DIR --generic-dir GENERIC_DIR.