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Converting genotypes to allele frequencies
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15 months ago
110300553 • 0

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

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11 months ago
JC 7.9k
Mexico

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, ...)

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