Functions to generate SNPs on given samples.

Functions to generate SNPs on given samples.

Usage

make_snp(samples, ss)

make_snp_chromosome(genealogy, segsites)

place_mutations(genealogy, segsites, v_sampled = NULL)

Arguments

samples

A data.frame: sample_family or output from gather_segments().

ss

A sequence of segsites; its length is the number of chromosome; each element is the number of segsites on a chromosome. If a named vector is given, the output is also named.

genealogy

An output from make_gene_genealogy().

segsites

The number of segregating sites on a segment.

v_sampled

The sampled vertices. Use this to fix the output order.

Details

make_snp() generates a list of SNP matrices by calling make_snp_chromosome() in parallel. Use RNGkind("L'Ecuyer-CMRG") and set.seed() to get reproducible results. The number of CPU cores used can be configured via mc.cores option.

make_snp_chromosome() simulate a SNP matrix on a chromosome by calling place_mutations() and recombination().

place_mutations() generates a SNP matrix by randomly placing a fixed number of mutations on a given genealogy. It means that all the sites are perfectly linked with each other.