Update to handle flipped reference alleles in dosage files (encoded 0 to 2) in predict_gene_expression.py

hakyim / TO-DELETE-PrediXcan

Code for the in-dev PrediXcan Project

MIT License

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Update to handle flipped reference alleles in dosage files (encoded 0 to 2) in predict_gene_expression.py #8

Closed hainswor closed 8 years ago

hainswor commented 8 years ago

Original Program's handling of flipped reference alleles operates for dosage files encoded -1, 0, 1 (continuous). This update would handle SNPs with flipped reference alleles with dosages encoded 0, 1, 2 (continuous). The 0:2 dosage format is used in PrediXcan example dosage files and produced if using the convert_plink_to_dosage.py script.

Hope this is helpful,

-Hannah C Ainsworth, Kip D Zimmerman, Carl D Langefeld from Wake Forest's Center for Public Health Genomics

hakyim commented 8 years ago

Thank you for the contribution. This has been merged to the hakyimlab/PrediXcan fork.