Converting csv or text files to ped and map file for GWAS

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3.0 years ago

JFeng • 0

Does anyone know how to convert csv or text file to ped and map format so that I could do association analysis using PLINK? What I have now is the phenotype and genotype matrix in csv.

Thanks!

plink GWAS • 1.6k views

ADD COMMENT • link updated 2.9 years ago by zx8754 11k • written 3.0 years ago by JFeng • 0

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PED and MAP files are text files, change your text/csv files to match the required format.

ADD REPLY • link 3.0 years ago by zx8754 11k

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I have tried to arrange my files to the required format and then changed the extension to '.ped' and '.map', but the problem still exists and it gives me error of half-missing call for variant 3 at line 1, and sometimes it gives me error for failed to open .

ADD REPLY • link 3.0 years ago by JFeng • 0

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Share the row of data that fails, also share the plink code you have tried.

ADD REPLY • link 2.9 years ago by zx8754 11k

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