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README.md
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@@ -91,13 +91,17 @@ Three complementary tables connect mutation data directly to the expression samp
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| META-PRISM | 354 | 567 | 124 |
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| DepMap | 1,465 | 100,850 | 18,608 |
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**Mutation definition
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**Sample matching
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**Missing data
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**Comparison panel
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## MONDO disease hierarchy
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| META-PRISM | 354 | 567 | 124 |
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| DepMap | 1,465 | 100,850 | 18,608 |
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**Mutation definition**
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Variants with `vep_impact` equal to `HIGH` or `MODERATE` were retained. Multiple qualifying variants in a gene were collapsed to binary presence. These tables describe mutation presence, rather than individual variants or allele frequencies.
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**Sample matching**
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Join by `dataset` and `sample_id`; `sample_id` matches the observation identifier in the corresponding H5AD. TCGA patient-level calls and META-PRISM subject-level calls were assigned to their expression samples. DepMap calls were matched to model identifiers. DepMap mutation data use **25Q3**, while expression data use **24Q4**.
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**Missing data**
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A sample present in `assayed_samples` but absent from `mutated_genes` has no qualifying mutation in the represented gene set. A sample absent from `assayed_samples` has no mutation data in this export.
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**Comparison panel**
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The intersection of the three mutation gene sets contains **124 genes**. The `assayed_genes` table records columns present in the input mutation matrices.
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## MONDO disease hierarchy
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