legacy_decode19: Legacy version of the 'decode19' map

In ibdsim2: Simulation of Chromosomal Regions Shared by Family Members

Legacy version of the decode19 map

Description

A legacy version of the built-in human recombination map, based on Halldorsson et al., 2019. The implementation of this map used in ibdsim2 was updated in v2.3.0, adding the physical endpoint of each chromosome (this was previously lacking), and using a better thinning algorithm to reduce the raw data given by Halldorsson et al. (2019). See also loadMap().

Usage

legacy_decode19

Format

A genomeMap object: a list of 23 chromMap objects. Each chromMap is a list containing two numeric matrices, named male and female, and carries these attributes:

• physStart – first physical position (Mb) on the chromosome

• physEnd – last physical position (Mb) on the chromosome

• physRange – physical length, physEnd - physStart (Mb)

• mapLen – length-2 numeric: centiMorgan length of male and female strands

• chrom – chromosome label

• Xchrom – logical flag used by simulators for X-inheritance

Examples

loadMap("decode19")         # new
loadMap("legacy_decode19")  # legacy

ibdsim2 documentation built on Aug. 22, 2025, 5:11 p.m.