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README.md

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GenEpi takes the [Genotype File Format](http://www.stats.ox.ac.uk/~marchini/software/gwas/file_format_new.html) (.GEN) used by Oxford statistical genetics tools, such as IMPUTE2 and SNPTEST as the input format for genotype data. If your files are in [PLINK format](https://www.cog-genomics.org/plink/1.9/formats) (.BED/.BIM/.FAM) or [1000 Genomes Project text Variant Call Format](https://www.cog-genomics.org/plink/1.9/formats#vcf) (.VCF), you could use [PLINK](https://www.cog-genomics.org/plink/1.9/) with the following command to convert the files to the .GEN file.
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If your files are in the **.BED/.BIM/.FAM** format.
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If your files are in the **.BED/.BIM/.FAM** format.
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```
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$ plink --bfile prefixOfTheFilename --recode oxford --out prefixOfTheFilename
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```
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**4\. Model Persistance**
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The final models of the step five and step six would be persisted in the folder **crossGeneResult** as **RFClassifier/Regressor.pkl** and **RFClassifier/Regressor_Covariates.pkl** respectively. You could load these models for future use without having to retrain.
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The final models of the step five and step six will be persisted in the folder **crossGeneResult** as **RFClassifier/Regressor.pkl** and **RFClassifier/Regressor_Covariates.pkl** respectively. You could load these models for future use without having to retrain.
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## Meta
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Chester (Yu-Chuan Chang) - [email protected]

setup.py

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setup(
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name = 'genepi',
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version = '1.0.4',
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version = '1.0.5',
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description = 'A package for detecting epsitasis by machine learning',
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long_description=long_description,
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long_description_content_type='text/markdown',
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'Topic :: Scientific/Engineering :: Bio-Informatics',
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'Topic :: Scientific/Engineering :: Artificial Intelligence',
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],
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keywords = ['epistasis', 'SNP-SNP interactions'],
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keywords = ['epistasis', 'SNP-SNP interactions', 'GWAS'],
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packages = ['genepi'],
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install_requires=[
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'pymysql>=0.8.0',

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