This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Converting genotypes to allele frequencies

I have a table of genotpyes (AA, GG, CT etc.) per sample and their corresponding rsids. I don't have any other corresponding files, just this .txt table, is there a way for me to batch convert these to allele counts in R(0,1,2)? I've found a lot of people doing this individually by SNP but I have 100K + rsids and want to examine them all.

snp genome r
• 1,564 views • link
updated by JC JC • written by 110300553 • 110300553

Can you provide example file, something like: myData[ 1:10, 1:10 ] ?

• 0 views • link
written by zx8754 zx8754

1 answer

You probably need to create a script that does the conversion, you can use the NCBI API (https://api.ncbi.nlm.nih.gov/variation/v0/#/) to query each rs and define which allele is the reference (0) and any other allel (1,2, ...)

• 0 views • link
written by JC JC

Log in to answer this question.

More posts like this