Evaluation of Genotyping Error in Genotype-by-Sequencing Data
return a `ggplot2' plot object of the posterior esimates for heterozyo...
just a quick function for making an 012 matrix from a character matrix
convert a VCF into an 012,-1 matrix and read_depth bin matrix for esti...
tidy up the estimate_m_rd output into something you can plot
whoa: Evaluation of genotyping error in genotype by sequencing data
bin read depths of SNPs into categories having at least S observations
Estimate heterozygote miscall rate for different read depth categories...
Computed expected and observed genotype frequencies from a `vcfR' obje...
function to return a tibble with the min/max values of genotype freqs ...
from on 012 file compute expected (assuming HW equilbrium) and observe...
return a `ggplot2' plot object of observed and expected genotype freqs
simulate a new miscall rate for each read depth category given X and Y
simulate new reference allele frequencies from their beta full conditi...
compute full conditional for each X given Y, p, R, and m, and then sam...
get posterior estimates for m from different read depth categories
This is a small, lightweight package that lets users investigate the distribution of genotypes in genotype-by-sequencing (GBS) data where they expect (by and large) Hardy-Weinberg equilibrium, in order to assess rates of genotyping errors and the dependence of those rates on read depth. It implements a Markov chain Monte Carlo (MCMC) sampler using 'Rcpp' to compute a Bayesian estimate of what we call the heterozygote miscall rate for restriction-associated digest (RAD) sequencing data and other types of reduced representation GBS data. It also provides functions to generate plots of expected and observed genotype frequencies. Some background on these topics can be found in a recent paper "Recent advances in conservation and population genomics data analysis" by Hendricks et al. (2018) <doi:10.1111/eva.12659>, and another paper describing the MCMC approach is in preparation with Gordon Luikart and Thierry Gosselin.