rrBLUP, Rsamtools, GenomeInfoDb, Biostrings, GenomicRanges,
VariantAnnotation, SummarizedExperiment, S4Vectors, IRanges,
BiocGenerics, knitr, rmarkdown, GenomicFeatures, qqman,
ggplot2, adegenet

rrBLUP, Rsamtools, GenomeInfoDb, Biostrings, GenomicRanges,
VariantAnnotation, SummarizedExperiment, S4Vectors, IRanges,
BiocGenerics, knitr, rmarkdown, GenomicFeatures, ggplot2,
adegenet

c(person("Lindsay V.", "Clark", email = "Lindsay.Clark@seattlechildrens.org",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-3881-9252")),
person("U.S. National Science Foundation", role = "fnd"))
Read depth data from genotyping-by-sequencing (GBS) or restriction
site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian
probability estimates of genotypes in polyploids or diploids.  The genotype
probabilities, posterior mean genotypes, or most probable genotypes can then
be exported for downstream analysis.  'polyRAD' is described by Clark et al.
(2019) <doi:10.1534/g3.118.200913>, and the Hind/He statistic for marker
filtering is described by Clark et al. (2022) <doi:10.1186/s12859-022-04635-9>.
A variant calling pipeline for highly duplicated genomes is also included and
is described by Clark et al. (2020, Version 1) <doi:10.1101/2020.01.11.902890>.

Simulate and test marker dosage for dominant markers in
autopolyploids
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
may be generated at random.

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 may be generated at random.

Simulate and Test Marker Dosage for Dominant Markers in
Autopolyploids