Add Emerson_CMV repertoire + metadata schema descriptions
Browse files
README.md
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@@ -89,6 +89,8 @@ sequenceStatus, estimatedNumberGenomes, sequence, num_reads, repertoire_id, part
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v_call, d_gene, j_call, sequenceStatus, v_family, d_family, j_family, v_resolved, d_resolved, j_resolved,
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sequence, num_reads`.
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## Metadata schemas
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All `metadata.tsv` files share `participant_label`, `specimen_label`, and `disease` (the classification target).
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@@ -100,6 +102,9 @@ Cross-validation fold assignments are provided per cohort (`CV_fold` / `fold` /
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fraction_productive, productive_simpson_clonality, sample_tags, sku, test_name`, …).
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- **Rawat_T1D**: subject clinical/HLA fields (`diabetes_status, sex, age, duration, HLA A/B/C/DPB1/DQB1/DRB1…,
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hla_high_risk_type, autoantibody statuses, ML_class`).
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## Usage
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v_call, d_gene, j_call, sequenceStatus, v_family, d_family, j_family, v_resolved, d_resolved, j_resolved,
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sequence, num_reads`.
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**Emerson_CMV** (minimal, 7 columns): `cdr3_aa, v_call, j_call, sequence, num_reads, repertoire_id, participant_label`.
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## Metadata schemas
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All `metadata.tsv` files share `participant_label`, `specimen_label`, and `disease` (the classification target).
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fraction_productive, productive_simpson_clonality, sample_tags, sku, test_name`, …).
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- **Rawat_T1D**: subject clinical/HLA fields (`diabetes_status, sex, age, duration, HLA A/B/C/DPB1/DQB1/DRB1…,
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hla_high_risk_type, autoantibody statuses, ML_class`).
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- **Emerson_CMV**: same base fields as Mal-ID/Mitchell_T1D (`specimen_time_point, study_name, available_gene_loci,
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disease_subtype, age, sex, ancestry`) plus `repertoire_file, emerson_subject_id, cohort, cohort_name, race,
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ethnicity, race_and_ethnicity, known_cmv_status, metadata_source`.
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## Usage
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