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Change plink file for logistic in R

Hi all,

I would like to extract single snp from plink to R for a logistic regression.

I used --recode and got map/ped file. Also, I used --make-bed and got binary file.

Please anyone navigate me how to change from those file to right format for running logistic in R

Any suggestions are appreciated.

Thanks

plink snp logistic r
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updated by zx8754 zx8754 • written by C-man • C-man

The r function convert.snp.ped from R package GenABEL.

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updated by Ram Ram • written by Genefan33 • Genefan33

1 answer

In PLINK you can use the --recodeA flag to output your data as a single data frame, where each SNP is coded as allele dose; one SNP per column.

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updated by Ram Ram • written by mbyvcm mbyvcm

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