How to open the genotype information in a bed file in R or Ubuntu
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3 months ago
Phylicia ▴ 10

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. enter image description 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. enter image description here

Could you give me some suggestions?Thanks a lot!

file genotype bed ubuntu R • 250 views
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3 months ago
Sam ★ 4.4k

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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Thanks a lot for your kind help, Sam.

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