R/vars_functions.R
vars_functions.RdThe 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_thetaUses an estimate for theta, the population-scaled mutation rate, and a desired number of variants.
vars_phyloUses phylogenetic tree(s) from phylo
object(s) or NEWICK file(s), one tree per chromosome or one for all
chromosomes.
vars_gtreesUses 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_ssitesUses matrices of segregating sites,
either in the form of
scrm or coala coalescent-simulator object(s), or
a ms-style output file.
vars_vcfUses a variant call format (VCF) file that directly specifies variants.