Tag Archives: genotypes

Allele frequency and genotype manipulation in R

As I am trying to wrap my dissertation up I am going over all my data and analyses again and  again. No need to say that every time I look at numbers and how I generated them something new wrong or unexpected always pops up. The other day, for example, I was working with some of the genotype files that I am using in my analyses. I was trying to review allele frequencies and calculate again multi-locus-heterozygosity. Since I was doing all of this in RStudio I finally forced myself to write an R function that would the hardest part of the job for me, and save me time and headaches.

I borrowed some code from here and adapted it for my purposes. The function takes a data frame containing microsatellite genotype information as input and does 2 major things: first it calculates allele frequencies and produces a graphical output; second, it formats the data so that they can be processed by another package, Rhh, for multi-locus-heterozygosity. The output of this function are two files that will be added to your global environment. The first file, named OUT contains the allele frequencies. The second file, named MyDataMLHready contains the data formatted for Rhh (review the Rhh help file to run the MLH analysis).

Take a look at the actual function here. Copy the text and run it on your R or RStudio to load the function in your working environment. You can download some microsatellite genotyped data from here and test the code yourself. You will have to import the .txt file in R.

If the function doesn’t work or you have suggestions on how to make it better or add new functionalities don’t hesitate to write a comment.