markers_on_map: An example of how to specify markers mapped onto chromosomes

In eriqande/CKMRsim: Inference of Pairwise Relationships Using Likelihood Ratios

An example of how to specify markers mapped onto chromosomes

Description

This is a named list. Each component is named with the number of the chromosome. In this case, those numbers are: "4", "9", "14", "19", and "21". Each component is itself a named list that holds the position in centiMorgans and the allele frequencies of the alleles at the marker.

Usage

markers_on_map

Format

A named list of chromosomes upon which mapped markers are available. The component corresponding to a chromome is itself a list which may or may not be named. If it is named then its names are the names of the loci. The loci should be in sorted order along the chromosome. Each locus within a chromosome is represented as a list with the following components.

pos

Position in centiMorgans along the chromosome. This is a little nonstandard, but you can think of the first locus as having a certain rate of recombination with the very beginning of the chromosome, and then pos is the cumulative sum of the inter-locus recombination fractions.

freqs

The allele frequencies at the locus

eriqande/CKMRsim documentation built on Aug. 2, 2024, 7:23 a.m.