simulCoalescent: Coalescent with recombination
In timflutre/rutilstimflutre: Timothee Flutre's personal R code

simulCoalescent

R Documentation

Coalescent with recombination

Description

Simulate haplotypes according to an approximation to the coalescent with recombination named the Sequential Coalescent with Recombination Model. Requires the scrm package (Staab et al, 2014).

Usage

simulCoalescent(
  nb.inds = 500,
  ind.ids = NULL,
  nb.reps = 10,
  pop.mut.rate = 40,
  pop.recomb.rate = 40,
  chrom.len = 5 * 10^5,
  other = NULL,
  nb.pops = 1,
  mig.rate = 5,
  get.trees = FALSE,
  get.tmrca = FALSE,
  get.alleles = FALSE,
  permute.alleles = TRUE,
  verbose = 1
)

Arguments

`nb.inds`	diploids (thus nb of haplotypes is 2 * nb.inds)
`ind.ids`	vector of identifiers (one per genotype)
`nb.reps`	number of independent loci that will be produced (could be seen as distinct chromosomes)
`pop.mut.rate`	theta = 4 N0 mu
`pop.recomb.rate`	rho = 4 N0 r
`chrom.len`	in bp
`other`	character vector of length 1 with other parameters to the simulator (e.g. time-specific parameters such as "-G 6.93 -eG 0.2 0.0 -eN 0.3 0.5")
`nb.pops`	number of populations (`kmeans` will then be used to pair haplotypes into diploid genotypes)
`mig.rate`	migration rate = 4 N0 m (will be symmetric)
`get.trees`	get gene genealogies in the Newick format
`get.tmrca`	get time to most recent common ancestor and local tree lengths
`get.alleles`	get fake alleles sampled in A,T,G,C
`permute.alleles`	if TRUE, the reference alleles are randomly chosen between ancestral and derived alleles
`verbose`	verbosity level (0/1/2)

Value

list with haplotypes (list), genotypes as allele doses (matrix) and SNP coordinates (data.frame)

Author(s)

Timothee Flutre

Examples

## Not run: ## simulate haplotypes and genotypes in a single population
nb.genos <- 200
Ne <- 10^4
chrom.len <- 10^5
mu <- 10^(-8)
c <- 10^(-8)
genomes <- simulCoalescent(nb.inds=nb.genos,
                           pop.mut.rate=4 * Ne * mu * chrom.len,
                           pop.recomb.rate=4 * Ne * c * chrom.len,
                           chrom.len=chrom.len)

## End(Not run)

timflutre/rutilstimflutre documentation built on Feb. 12, 2025, 11:35 p.m.