R/xoi User Guide

R/xoi is an R package for the analysis of crossover interference in experimental crosses, particularly regarding the gamma model. It has a rather disparate set of functions, which here I seek to organize and explain.

Estimates from crossover count data

• countxo - calculate the numbers of crossovers in backcross data.

• chiasma - estimate the distribution of the number of chiasmata, given crossover count data and the assumption of no chromatid interference, and assuming either a Poisson or unconstrained distribution, and with or without an obligate chiasma.

Estimates from crossover location data

• find.breaks - estimate crossover locations in a backcross.

• convertxoloc - convert the crossover location data from the format produced by find.breaks() to that needed for fitGamma().

Estimate the recombination rate along chromosomes

• est.recrate - obtain a smoothed estimate of the recombination rate along a chromosome, from the cM and Mbp positions of markers.

• recrate2scanone - convert the output of est.recrate() in the the format output by qtl::scanone(), so it can be plotted with qtl::plot.scanone().

• intensity - an estimate of the intensity function along a chromosome, from data on a backcross; goes with coincidence().

Measures of interference

• est.coi - estimate the coincidence function from backcross data.

• coincidence - an alternative estimate of the coincidence function from backcross data.

• est.coi.um - estimate the coincidence as a function of micron distance.

• kfunc - estimate the one-dimensional version of Ripley’s K function.

Data and simulation

• bssbsb - data from a pair of mouse backcrosses, B6 × Spret.

• simStahl - simulate data from the Stahl model, an extension to the Gamma model where crossovers come from the superposition of two processes, one with crossover interference and one without.

Fit Gamma and Stahl models

• fitGamma - fit the gamma model for crossover interference from data on crossover locations.

• fitStahl - fit the gamma model for crossover interference from data on crossover locations.

• stahlLoglik - calculate the log likelihood for the Stahl model, with data on crossover locations.

Calculations related to the Gamma model

• xoprob - probability distribution of the number of crossovers for a chromosome of a given length, for the gamma model.

• ioden - the density of the distance from a given crossover to the next crossover, for the gamma model.

• location.given.one - calculate the density function for the location of the crossover given that there is precisely one, for the gamma model.

• distance.given.two - the density function for the distance between the two crossovers given that there are exactly two, for the gamma model.

• joint.given.two - the joint density function for the locations of two crossovers given that there are exactly two, for the gamma model.

• firstden - the density function of the distance from an arbitrary point to the next crossover, for the gamma model.

• first.given.two - the density function for the location of the first crossover given that there are exactly two, for the gamma model.

• gammacoi - the coincidence function for the gamma model.

• stahlcoi - the coincidence function for the Stahl model.

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    Karl Broman