How to make genotype from allele data

Question

[mirzaei86.vahid]

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

Answer 1

[Petr Ponomarenko]

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

• https://cran.r-project.org/web/packages/HardyWeinberg/HardyWeinberg.pdf
• https://cran.r-project.org/web/packages/genetics/genetics.pdf
• https://cran.r-project.org/web/packages/adegenet/adegenet.pdf
• ftp://cran.r-project.org/pub/R/web/packages/hierfstat/hierfstat.pdf
• https://cran.r-project.org/web/packages/pegas/pegas.pdf

and many more.

[mirzaei86.vahid]

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:

[Petr Ponomarenko]

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.