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R/simcross

Karl W Broman


R/simcross is an R package for simulating and plotting general experimental crosses.


Installation

You can install R/simcross from CRAN:

install.packages("simcross")

Vignette

A vignette describing the use of the package is available from within R (and also here). Load the package and then use the vignette function.

library(simcross)
vignette("simcross", package="simcross")

License

This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.

A copy of the GNU General Public License, version 3, is available at https://www.r-project.org/Licenses/GPL-3

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Version

Install

install.packages('simcross')

Monthly Downloads

191

Version

0.6

License

GPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Karl Broman

Last Published

November 29th, 2023

Functions in simcross (0.6)

sim_ail_pedigree_fix_n

Simulate AIL pedigree with fixed n
sim_crossovers

Simulate crossover locations using the Stahl model
convert2geno_allchr

Convert continuous allele information into marker genotypes for multiple chromosomes
create_parent

Create a parent object
cross

Cross two individuals
plot_crosslines

Plot cross lines
get_geno

Get genotype at a single position
plot_ind

Plot an individual
mouseL_cox

Mouse chromosome lengths
mouseL_mgi

Mouse chromosome lengths
sim_dof1_pedigree

Simulate pedigree for F1 between diversity outbreds and another inbred line
sim_from_pedigree

Simulate genotypes for pedigree
AILped

Example AIL pedigree
CCcolors

Collaborative Cross colors
sim_do_pedigree

Simulate a pedigree for Diversity Outbred mice
calc_Lstar

Calculate adjusted chromosome length for obligate chiasma
check_pedigree

Check a pedigree for errors
sim_4way_pedigree

Simulate pedigree for 4-way intercross
sim_ail_pedigree

Simulate AIL pedigree
collapse_do_alleles

Collapse alleles for simulated DO genotypes
sim_do_pedigree_fix_n

Simulate a pedigree for Diversity Outbreds for a target sample size
sim_from_pedigree_allchr

Simulate genotypes for pedigree for multiple chromosomes
convert2geno

Convert continuous allele information into marker genotypes
sim_ril_pedigree

Generate a ril pedigree
where_het

Find heterozygous regions
sim_meiosis

Simulate meiosis