Open gregorgorjanc opened 1 year ago
gregorgorjanc
commented
1 year ago [ ] How recombination is modelled (gamma-sprinkling) https://github.com/gaynorr/AlphaSimR/issues/94 https://github.com/gaynorr/AlphaSimR/discussions/89
[ ] describe the data structure in recHist https://github.com/gaynorr/AlphaSimR/issues/53
gregorgorjanc
commented
1 year ago Mention
[ ] This paper describes a software that infers parameters of the gamma-sprinkling model: CODA (crossover distribution analyzer): quantitative characterization of crossover position patterns along chromosomes https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-27
[ ] Genetic Map Functions https://onlinelibrary.wiley.com/doi/full/10.1002/0470011815.b2a05037
[ ] Two Types of Meiotic Crossovers Coexist in Maize https://doi.org/10.1105/tpc.109.071514
[ ] Exploring impact of recombination landscapes on breeding outcomes https://www.pnas.org/doi/full/10.1073/pnas.2205785119
gregorgorjanc
commented
1 month ago @AprilYUZhang can you please help us with this vignette? I suggest you: 1) Fork this repository 2) Copy the basic vignette 3) Port the example shown in https://github.com/gaynorr/AlphaSimR/issues/34 4) Weave in other bits mentioned in this issue https://github.com/gaynorr/AlphaSimR/blob/master/vignettes/intro.Rmd
Is your feature request related to a problem? Please describe. There is no documentation how recombinations are simulated.
Describe the solution you'd like A short vignette describing the implemented recombination model and how recombination information is stored in recHist would be very valuable for the community.
Additional context
The current AlphaSimR version uses the gamma sprinkling model to model recombination. An older version used just the gamma model and even older versions used the count-location model. There is no really great introduction to how these models work. The count-location and gamma models are referenced in this slide deck by Karl Broman. He also provides several relevant citations in the last slides. You can get a little more details about the gamma sprinkling model in this paper which deals with estimating crossover interference. The default values for AlphaSimR’s gamma sprinkling model set all crossovers coming from the crossover interference pathway with the interference parameter set to 2.6. These values roughly correspond to the crossover interreference assumed by the Kosambi mapping function.