sigmutselcovs covariate matrices: TCGA-THCA

Pre-built per-gene covariate matrices for TCGA-THCA (Thyroid carcinoma (TCGA-THCA: papillary thyroid carcinoma, from thyroid follicular epithelial cells). GTEx maps to Thyroid (representative gtex_thyroid). TCGA ATAC-seq covered (Corces et al. 2018; the tarball's bigWigs are named THCA_..., read from its first member). Expression: TCGA-THCA tumor and normal (59 solid-tissue normals, so the default Tumor+Normal pair stays). Roadmap null: none of its 127 epigenomes is thyroid. encode_chromatin: adult thyroid gland tissue from one ENTEx donor (ENCDO271OUW, female, 51y; THCA is about three-quarters female, so a female donor matches the cohort's chrX state) -- H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9me3 and DNase, all single-replicate. Three other adult donors (ENCDO845WKR male 37y, ENCDO451RUA male 54y, ENCDO793LXB female 53y, the last without H3K27me3) carry the same panel and are left out to keep one donor. No thyroid cell line has usable chromatin in ENCODE: K1 (the only thyroid-carcinoma line there, and an ICLAC-listed GLAG-66 derivative) has only a RAD21 ChIA-PET; TPC-1, B-CPAP, 8505C, FTC-133, Nthy-ori 3-1 return nothing. repliseq null: nothing in the replication-timing catalog is thyroid or follicular epithelium; the hESC-derived posterior-foregut endocrine Repli-chip profile is embryonic and pancreatic-lineage, rejected. GENERIC's pooled RT covers it. Assemblies: encode_chromatin and ATAC GRCh38.), 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 1099 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 THCA --data-dir DIR --generic-dir GENERIC_DIR.