Question: Converting genotypes to allele frequencies
0
gravatar for 110300553
6 months ago by
1103005530
1103005530 wrote:

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 R genome • 192 views
ADD COMMENTlink modified 6 months ago by JC8.2k • written 6 months ago by 1103005530

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

ADD REPLYlink written 6 months ago by zx87547.9k
1
gravatar for JC
6 months ago by
JC8.2k
Mexico
JC8.2k wrote:

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, ...)

ADD COMMENTlink written 6 months ago by JC8.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 542 users visited in the last hour