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

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.

The error report in R is here.

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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.

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Could you give me some suggestions? Thanks a lot!

ubuntu bed genotype r
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updated by Ram Ram • written by Phylicia • Phylicia

1 answer

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.

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written by Sam Sam

Thanks a lot for your kind help, Sam.

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written by Phylicia • Phylicia

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