haps_functions {jackalope}

Organize higher-level information for creating haplotypes.

Description

The following functions organize information that gets passed to create_haplotypes to generate haplotypes from a reference genome. Each function represents a method of generation and starts with "haps_". The first three are phylogenomic methods, and all functions but haps_vcf will use molecular evolution information when passed to create_haplotypes.

Details

haps_theta

Uses an estimate for theta, the population-scaled mutation rate, and a desired number of haplotypes.

haps_phylo

Uses phylogenetic tree(s) from phylo object(s) or NEWICK file(s), one tree per chromosome or one for all chromosomes.

haps_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.

haps_ssites

Uses matrices of segregating sites, either in the form of scrm or coala coalescent-simulator object(s), or a ms-style output file.

haps_vcf

Uses a haplotype call format (VCF) file that directly specifies haplotypes.

See Also

create_haplotypes