How to open the genotype information in a bed file in R or Ubuntu

Question

[Phylicia]

My question is that how could I open a bed file and see the individual genotype?

I searched the two posts previously, but they did not work.

• reading a bed file in R
• is it possible to know individual genotype(alleles) by SNP in plink?

The error report in R is here.

I also tried using Plink. But it says the column of map file is not right. So I rename the columns in map file, but it does not work, either.

Could you give me some suggestions? Thanks a lot!

Answer 1

[Sam]

PLINK bed files are binary, and it cannot be read directly into R using read.table. You can use specific packages like bigsnpr. As for why your PLINK code does not work, you should use --bfile instead of --file as your files are already in the bed bim fam format, instead of the ped map format.

[Phylicia]

Thanks a lot for your kind help, Sam.