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How to make genotype from allele data

Hi

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?

Thanks

snp r gene
• 2,487 views • link
written by mirzaei86.vahid • mirzaei86.vahid

1 answer

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.

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written by Petr Ponomarenko Petr Ponomarenko

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

• 0 views • link
written by mirzaei86.vahid • mirzaei86.vahid

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.

• 0 views • link
written by Petr Ponomarenko Petr Ponomarenko

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