In this short blog post, I’m gonna show you a super simple way to calculate genotype frequencies. Let’s say we’re looking at a single spot in the DNA (a biallelic situation) with two possible versions, “A” and “a”. That means we can have three possible genotype combos: “AA”, “Aa”, and “aa”. What we want to do is count how many times each of these genotypes shows up at each SNP. ...
Here, I introduce an R function for calculating minor allele frequencies (MAF). calcmaf <- function(M, col1ID = TRUE) { if(col1ID) { maf = colMeans(M[,-1])/2 } else { maf = colMeans(M)/2 } maf[maf > 0.5] <- 1 - maf[maf > 0.5] return(unname(maf)) } The calcMAF function takes arguments M and col1ID. M is the genotype data frame with genotypes coded as 0:2. col1ID takes TRUE or FALSE. If TRUE (default) the 1st column of M is animal ID. Let’s create an example genotype data frame for 10 genotypes and 20 SNPs, where the first column is animal ID. ...
A basic YAML header to start with. Choose the desired output format. --- title: "RMarkdown Example" author: "Mohammad Ali Nilforooshan" date: "6 August 2017" output: html_document # output: pdf_document # output: word_document --- ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE) ``` horizontal rule *** or --- Formatting Manual line break: End the line with two or more spaces. italic *italic* and italic _italic_ bold **bold** and bold __bold__ superscript2 superscript^2^ subscript2 subscript~2~ ...