使用R代替下一代测序vcf文件

I am an R beginner. I am using R to analyse my large next-generation sequencing vcf file and am having some difficulties. I have imported the very large vcf file as a data frame (2446824 obs. of 177 variables) and made a subset with just the 3 samples I am interested in (2446824 obs. of 29 variables).I am an R beginner. I am using R to analyse my