haps_ssites: Organize information to create haplotypes using segregating...

In jackalope: A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator

Organize information to create haplotypes using segregating sites matrices

Description

This function organizes higher-level information for creating haplotypes from matrices of segregating sites output from coalescent simulations.

Usage

haps_ssites(obj = NULL, fn = NULL)

Arguments

obj

Object containing segregating sites information. This can be one of the following: (1) A single list with a seg_sites field inside. This field must contain a matrix for segregating sites for each chromosome. The matrix itself should contain the haplotype information, coded using 0s and 1s: 0s indicate the ancestral state and 1s indicate mutant. The matrix column names should indicate the positions of the polymorphisms on the chromosome. If positions are in the range ⁠(0,1)⁠, they're assumed to come from an infinite- sites model and are relative positions. If positions are integers in the range ⁠[0, chromosome length - 1]⁠ or ⁠[1, chromosome length]⁠, they're assumed to come from an finite-sites model and are absolute positions. Defaults to NULL.

fn

A single string specifying the name of the file containing the ms-style coalescent output with segregating site info. Defaults to NULL.

Details

For what the seg_sites field should look like in a list, see output from the scrm or coala package. (These packages are not required to be installed when installing jackalope.) If using either of these packages, I encourage you to cite them. For citation information, see output from citation("scrm") or citation("coala").

Value

A haps_ssites_info object containing information used in create_haplotypes to create variant haplotypes. This class is just a wrapper around a list of matrices of segregating site info, which you can view (but not change) using the object's mats() method.

jackalope documentation built on Oct. 15, 2023, 9:06 a.m.