Question: How to make genotype from allele data
gravatar for mirzaei86.vahid
2.3 years ago by
mirzaei86.vahid30 wrote:


I have a data which composed of allele information homo, hetero ; normal,disease and etc.

Each patient has this information, a table with several columns looks like :

Patient  SNP1    SNP2

P1   AA      0    

P2   Ab      1

P3   BB      0

My question is, Does R has any packages for calculating genotype groups and allele frequency?


snp R gene • 836 views
ADD COMMENTlink written 2.3 years ago by mirzaei86.vahid30
gravatar for Petr Ponomarenko
2.3 years ago by
United States / Los Angeles /
Petr Ponomarenko2.6k wrote:

What is the last column in your input with 0 and 1. Why R and what questions you are going to studt with it? plink is popular genotype data analysis. There is a way to use plink from inside R =) As always with R there are packages dedicated for very specific tasks like

and many more.

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Petr Ponomarenko2.6k

Thanks @Petr Ponomarenko. The last column is another representation of my SNP columns. And about your second question, I'm more familiar with R, I have no information about PLINK.

Can I use PLINK for Sanger SNP data like this:

enter image description here

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by mirzaei86.vahid30

this apears to me as a screenshot with no structure. just numbers in a box =) What are the columns, rows and data types? Please describe the dataset.

R is great, but plink might be easier to go around reviewers since it has a lot of different statistical models and tests inside and ways to format data in popular ways.

ADD REPLYlink written 2.3 years ago by Petr Ponomarenko2.6k
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