recomb_map_hg

recomb_map_hg38

recomb_map_hg37

Human genetic recombination maps for builds 38 (GRCh38/hg38) and 37 (GRCh37/hg19, below suffixed as hg37 for simplicity although technically incorrect).
Processed each first with <code>recomb_map_fix_ends_chr()</code> to shift and extrapolate to sequence ends, then simplified with <code>recomb_map_simplify_chr()</code> to remove all values that can be extrapolated with an error of up to <code>tol = 0.1</code>, in order to reduce their sizes and interpolation runtime.
Defaults were used, which resulted in extrapolated recombination rates close to and centered around the average of 1e-6 cM/base).
Autosomes only.

datasets

The focus is on simulating and modeling families with founders drawn from a structured population (for example, with different ancestries or other potentially non-family relatedness), in contrast to traditional pedigree analysis that treats all founders as equally unrelated. Main function simulates a random pedigree for many generations, avoiding close relatives, pairing closest individuals according to a 1D geography and their randomly-drawn sex, and with variable children sizes to result in a target population size per generation. Auxiliary functions calculate kinship matrices, admixture matrices, and draw random genotypes across arbitrary pedigree structures starting from the corresponding founder values. The code is built around the plink FAM table format for pedigrees. Described in Yao and Ochoa (2022) <doi:10.1101/2022.03.25.485885>.

Alejandro Ochoa

simfam

Simulate and Model Family Pedigrees with Structured Founders

recomb_map_hg function

A list with 22 elements (autosomes, not named), each a tibble with two columns defining the recombination map at that chromosome:<ul>
<li><code>pos</code>: position in base pairs</li>
<li><code>posg</code>: position in centiMorgans (cM)</li>
</ul>An object of class <code>list</code> of length 22.

Format

Simplified recombination maps for human genomes — recomb_map_hg

A list with 22 elements (autosomes, not named), each a tibble with two columns defining the recombination map at that chromosome:<ul>
<li><code>pos</code>: position in base pairs</li>
<li><code>posg</code>: position in centiMorgans (cM)</li>
</ul>

An object of class <code>list</code> of length 22.

recomb_map_hg: Simplified recombination maps for human genomes

Description

Usage

Arguments

Format