BiocGenerics, knitr, rmarkdown, GenomicFeatures, qqman,

Imports: fastmatch, pcaMethods, Rcpp, stringi

BiocGenerics, knitr, rmarkdown, GenomicFeatures, ggplot2,

Authors@R: c(person("Lindsay V.", "Clark", email = "Lindsay.Clark@seattlechildrens.org",
Maintainer: Lindsay V. Clark <Lindsay.Clark@seattlechildrens.org>
(2019) <doi:10.1534/g3.118.200913>, and the Hind/He statistic for marker
A variant calling pipeline for highly duplicated genomes is also included and

Title: Simulate and test marker dosage for dominant markers in
Description: Perform classic chi-squared tests and Ripol et al(1999)
binomial confidence interval approach for autopolyploid
dominant markers. Also, dominant markers may be generated for
families of offspring where either one or both of the parents
possess the marker. Missing values and misclassified markers

dominant markers. Also, dominant markers may be generated
for families of offspring where either one or both of the
parents possess the marker. Missing values and
misclassified markers may be generated at random.

Title: Simulate and Test Marker Dosage for Dominant Markers in

Title: Bayesian mixture models for marker dosage in autopolyploids
Description: Fits Bayesian mixture models to estimate marker dosage for
dominant markers on autopolyploids using JAGS (1.0 or greater).
May be used in conjunction with polySegratio for simulation
studies and comparison with standard methods

dominant markers on autopolyploids using JAGS (1.0 or greater)
as outlined in Baker et al (2010). May be used in conjunction
with polySegratio for simulation studies and comparison with

Depends: R (>= 2.12.0), polySegratio, coda

Description: Fits Bayesian mixture models to estimate marker dosage for dominant markers on autopolyploids using JAGS (1.0 or greater) as outlined in Baker et al (2010). May be used in conjunction with polySegratio for simulation studies and comparison with standard methods.

Title: Bayesian Mixture Models for Marker Dosage in Autopolyploids
Authors@R: c(person("Peter", "Baker", role = c("aut", "cre"),
Description: Fits Bayesian mixture models to estimate marker dosage for dominant markers in autopolyploids using JAGS (1.0 or greater) as outlined in Baker et al "Bayesian estimation of marker dosage in sugarcane and other autopolyploids" (2010, <doi:10.1007/s00122-010-1283-z>). May be used in conjunction with polySegratio for simulation studies and comparison with standard methods.