create_segsites: Segregating Sites

Description

This functions allow the creation and modification of segregating sites objects, which are on of the most basic statistics that is calculated in coala. Segregating Sites are primarily a matrix, where each row repesents a haplotype and each column represents a SNPs. A given entry is either 1 if the haplotype carries the derived allele for the SNP, or 0 if it carries the ancestral one.

Usage

create_segsites(snps, positions, trio_locus = numeric(0), check = TRUE)
get_snps(segsites)
get_positions(segsites)
set_positions(segsites, positions)
get_trio_locus(segsites)
set_trio_locus(segsites, trio_locus)
is_segsites(segsites)

Arguments

snps

The SNP Matrix

positions

A numeric vector indicating the relative positions of each SNP on the locus.

trio_locus

If the locus consists of a locus trio, then this contains the trio locus each SNP belongs to.

check

Whether non-segregating sites are remove from the segregating sites (TRUE) or not (FALSE).

segsites

The segregating sites object

Functions

get_snps: Returns the SNP matrix from a segregating sites object.
get_positions: Returns the SNP's positions from a segregating sites object.
set_positions: Sets the SNP's positions in a segregating sites object.
get_trio_locus: Returns the trio locus positions from a segregating sites object.
set_trio_locus: Sets the trio locus in a segregating sites object.
is_segsites: Checks whether an object is a segsites object.