cash-rf_2pt: BC, FS, and IC method: Compute 2-point recombination fraction...

In tpbilton/GUSMap: Genotyping Uncertainty with Sequencing Data and Linkage Mapping (GUSMap)

BC, FS, and IC method: Compute 2-point recombination fraction estimates and LOD scores

Description

Method for estimating 2-point recombination fraction and associated LOD scores.

Usage

BCobj$rf_2pt(nClust = 2, err = FALSE)
FSobj$rf_2pt(nClust = 2, err = FALSE)
ICobj$rf_2pt(nClust = 2, err = FALSE)

Arguments

nClust	An integer value for the number of cores to use in the parallelization of computing the 2-point recombination fraction estimates.
err	Locial value. If TRUE, a sequencing error parameter is also estimated as part of the 2-point recombination fraction estimates. If FALSE, then the sequencing error parameter is fixed at zero.

Details

In this function, the recombination fraction for all pairs of SNPs is computed. Estimation is performed by optimimizing the hidden Markov model (HMM) likelihood given by \insertCitebilton2018genetics1;textualGUSMap for two markers, where the parental phase that is used is the one that maximizes the likelihood, given the segregation type that has been inferred. The err specifies whether sequencing errors should also be estimated when computing the 2-point recombination fraction estimates. LOD scores associated with each pair of SNPs are also computed.

Parallelization is used to speed up the estimation process using the foreach function. The argument nClust specifies the number of cores to use in the parallelization. Note: It is important that the number of cores you specify is not more than what is available on your comupter (otherwise bad things can happen!).

Currently, only 2-point recombination fractions for a single population/family can be computed. However, there are plans to extend this function to multiple families in the future.

Note: This function can take a while, espically when there are a large number of SNPs.

Author(s)

Timothy P. Bilton

References

\insertRef

bilton2018genetics1GUSMap

See Also

BC, FS, IC

Examples

## simulate some sequencing data
set.seed(6745)
config <- list(list(sample(c(1,2,4), size=30, replace=TRUE)))
F1data <- simFS(0.01, config=config, meanDepth=10, nInd=50)

## Compute 2-point recombination fractions
F1data$rf_2pt(nClust=1)

tpbilton/GUSMap documentation built on Feb. 22, 2025, 12:27 p.m.