How to import impute2.dosage files to analyse it in R (GWAS)

Question

[Sebastian]

Hello all.

I want to do a Poisson regression, I have a dataset of 1800 people with 9m SNPs each. First of all, I'm having some trouble importing the info of each SNP, I tried using "gawk" in R (output <- system(tgawk 'NR==1{print$0}' data.impute2.dosage, intern=TRUE) but having each SNP info takes 2 seconds, so it would take almost a year to take each SNP and test it... Do you know a faster way to do the import? if you also know a fast way to do the poisson regression I would be grateful.

Thanks a lot!