I have a 905460 snp genotype data with 1096 patients, I have used the "HardyWeinberg" R package and removed the maf that is less than 0.05, the data reduced to 746907, then I applied the HWexact test using alpha as 0.001 and the data reduced to 384660.
Is this OK? or too much data was lost
I'm doing GWAS analysis and the data was provided by my advisor it is about Brest Cancer
Please help me and recommend what should I do