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R/xoi

R/xoi is an R package for the analysis of crossover interference in experimental crosses, particularly regarding the gamma model.


Installation

Install the R/xoi package from R universe:

install.packages("xoi", repos="https://kbroman.r-universe.dev")

Alternatively, use remotes to install it from its GitHub source:

install.packages("remotes")
library(remotes)
install_github("kbroman/xoi")

Vignette

A vignette describing the functions in the package is available on the web.


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('xoi')

Monthly Downloads

260

Version

0.76

License

GPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Karl Broman

Last Published

July 18th, 2026

Functions in xoi (0.76)

xoprob

Distribution of number of crossovers
recrate2scanone

Convert recrate to scanone format
xoi-package

xoi: Tools for Analyzing Crossover Interference
xoiversion

Installed version of R/xoi
intensity

Estimate intensity function
simStahl

Simulate crossover locations under the Stahl model
stahlcoi

Coincidence function for the Stahl model
stahlLoglik

Calculate log likelihood for Stahl model
est.coi

Estimate the coincidence function
find.breaks

Estimate crossover locations
countxo

Estimate number of crossovers
firstden

Distance to a crossover
gammacoi

Coincidence function for the gamma model
distance.given.two

Distance between crossovers given there are two
est.coi.um

Estimate the coincidence as a function of micron distance
first.given.two

Location of first crossover given there are two
joint.given.two

Crossover locations given there are two
coincidence

Estimate coincidence function
kfunc

estimate Ripley's K function
chiasma

Estimate chiasma distribution from crossover counts
bssbsb

BSS/BSB backcross data
convertxoloc

Convert format of crossover locations data
est.recrate

Estimate recombination rate
ioden

Distance between crossovers
fitStahl

Fit Stahl model
location.given.one

Location of crossover given there is one
fitGamma

Fit Gamma model