Simulates mutations within a genlight object

This script is intended to be used within the simulation framework of dartR. It adds the ability to add a constant mutation rate across all loci. Only works currently for biallelic data sets (SNPs). Mutation rate is checking for all alleles position and mutations at loci with missing values are ignored and in principle 'double mutations' at the same loci can occur, but should be rare.

Usage

gl.sim.mutate(x, mut.rate = 1e-06)

Arguments

x

Name of the genlight object containing the SNP data [required].

mut.rate

Constant mutation rate over nInd*nLoc*2 possible locations [default 1e-6]

Value

Returns a genlight object with the applied mutations

Author

Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

Examples

b2 <- gl.sim.mutate(bandicoot.gl,mut.rate=1e-4 )
#check the mutations that have occurred
table(as.matrix(bandicoot.gl), as.matrix(b2))
#>    
#>         0     1     2
#>   0 53408     4     0
#>   1     3 30692     0
#>   2     0     1 10187