Change plink file for logistic in R

Question

[C-man]

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

[Genefan33]

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

Answer 1

[christopher medway]

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.