update readme for return values
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README.md
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@@ -26,17 +26,17 @@ specific kwargs, if applicable, are mentioned in the sections below.<br>
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*Note that as you increase the context length to very large numbers you may start to reduce the size of the dataset since a large context size may
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cause indexing outside the boundaries of chromosomes.
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| Task | `task_name` | Sample Output
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| Variant Effect Causal eQTL | `variant_effect_causal_eqtl` | {ref sequence, alt sequence, label, tissue, chromosome,position, distance to nearest TSS} | SNP Classification | 1 | 88717 | 8846 | GTEx (via [Enformer](https://www.nature.com/articles/s41592-021-01252-x)) |
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| Variant Effect Pathogenic ClinVar | `variant_effect_pathogenic_clinvar` | {ref sequence, alt sequence, label, chromosome, position}
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| Variant Effect Pathogenic OMIM | `variant_effect_pathogenic_omim` | {ref sequence, alt sequence, label,chromosome, position}
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| CAGE Prediction | `cage_prediction` | {sequence, labels, chromosome}
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| Bulk RNA Expression | `bulk_rna_expression` | {sequence, labels, chromosome,position}
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| Chromatin Features Histone_Marks | `chromatin_features_histone_marks` | {sequence, labels,chromosome, position}
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| Chromatin Features DNA_Accessibility | `chromatin_features_dna_accessibility` | {sequence, labels,chromosome, position}
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| Regulatory Elements Promoter | `regulatory_element_promoter` | {sequence, label,chromosome, start, stop}
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| Regulatory Elements Enhancer | `regulatory_element_enhancer` | {sequence, label,chromosome, start, stop}
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## Usage Example
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```python
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*Note that as you increase the context length to very large numbers you may start to reduce the size of the dataset since a large context size may
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cause indexing outside the boundaries of chromosomes.
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| Task | `task_name` | Sample Output | ML Task Type | # Outputs | # Train Seqs | # Test Seqs | Data Source |
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|-------|-------------|-------------------------------------------------------------------------------------------|-------------------------|-------------|--------------|----------- |----------- |
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| Variant Effect Causal eQTL | `variant_effect_causal_eqtl` | {ref sequence, alt sequence, label, tissue, chromosome,position, distance to nearest TSS} | SNP Classification | 1 | 88717 | 8846 | GTEx (via [Enformer](https://www.nature.com/articles/s41592-021-01252-x)) |
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| Variant Effect Pathogenic ClinVar | `variant_effect_pathogenic_clinvar` | {ref sequence, alt sequence, label, chromosome, position} | SNP Classification | 1 | 38634 | 1018 | ClinVar, gnomAD (via [GPN-MSA](https://www.biorxiv.org/content/10.1101/2023.10.10.561776v1)) |
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| Variant Effect Pathogenic OMIM | `variant_effect_pathogenic_omim` | {ref sequence, alt sequence, label,chromosome, position} | SNP Classification | 1 | - | 2321473 |OMIM, gnomAD (via [GPN-MSA](https://www.biorxiv.org/content/10.1101/2023.10.10.561776v1)) |
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| CAGE Prediction | `cage_prediction` | {sequence, labels, chromosome,label_start_position,label_stop_position} | Binned Regression | 50 per bin | 33891 | 1922 | FANTOM5 (via [Basenji](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008050)) |
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| Bulk RNA Expression | `bulk_rna_expression` | {sequence, labels, chromosome,position} | Seq-wise Regression | 218 | 22827 | 990 | GTEx, FANTOM5 (via [ExPecto](https://www.nature.com/articles/s41588-018-0160-6)) |
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| Chromatin Features Histone_Marks | `chromatin_features_histone_marks` | {sequence, labels,chromosome, position, label_start_position,label_stop_position} | Seq-wise Classification | 20 | 2203689 | 227456 | ENCODE, Roadmap Epigenomics (via [DeepSea](https://pubmed.ncbi.nlm.nih.gov/30013180/) |
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| Chromatin Features DNA_Accessibility | `chromatin_features_dna_accessibility` | {sequence, labels,chromosome, position, label_start_position,label_stop_position} | Seq-wise Classification | 20 | 2203689 | 227456 | ENCODE, Roadmap Epigenomics (via [DeepSea](https://pubmed.ncbi.nlm.nih.gov/30013180/)) |
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| Regulatory Elements Promoter | `regulatory_element_promoter` | {sequence, label,chromosome, start, stop, label_start_position,label_stop_position} | Seq-wise Classification | 1| 953376 | 96240 | SCREEN |
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| Regulatory Elements Enhancer | `regulatory_element_enhancer` | {sequence, label,chromosome, start, stop, label_start_position,label_stop_position} | Seq-wise Classification | 1| 1914575 | 192201 | SCREEN |
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## Usage Example
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```python
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