R/vars_functions.R
vars_functions.Rd
The following functions organize information that gets passed to create_variants
to generate variants from a reference genome.
Each function represents a method of generation and starts with "vars_"
.
The first three are phylogenomic methods, and all functions but vars_vcf
will use molecular evolution information when passed to create_variants
.
vars_theta
Uses an estimate for theta, the population-scaled mutation rate, and a desired number of variants.
vars_phylo
Uses phylogenetic tree(s) from phylo
object(s) or NEWICK file(s), one tree per chromosome or one for all
chromosomes.
vars_gtrees
Uses gene trees, either in the form of
an object from the scrm
or coala
package or
a file containing output in the style of the ms
program.
vars_ssites
Uses matrices of segregating sites,
either in the form of
scrm
or coala
coalescent-simulator object(s), or
a ms
-style output file.
vars_vcf
Uses a variant call format (VCF) file that directly specifies variants.