snpdat

Contains counts of reference alleles and total read counts from the GBS data of Shirasawa et al (2017) for
the three SNP's used as examples in Gerard et. al. (2018).

datasets

Implements empirical Bayes approaches to genotype
polyploids from next generation sequencing data while
accounting for allelic bias, overdispersion, and sequencing
error. The main function is flexdog(), which allows the specification
of many different genotype distributions. An experimental
function that takes into account varying levels of relatedness
is implemented in mupdog(). Also provided are functions to
simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as
functions to calculate oracle genotyping error rates, oracle_mis(), and
correlation with the true genotypes, oracle_cor(). These latter two
functions are useful for read depth calculations. Run
browseVignettes(package = "updog") in R for example usage. See
Gerard et al. (2018) <doi:10.1534/genetics.118.301468> and
Gerard and Ferrao (2019) <doi:10.1093/bioinformatics/btz852> for details
on the implemented methods.

David Gerard

updog

Flexible Genotyping for Polyploids

snpdat function

A <code><a rd-options="tibble" href="/link/tibble?package=updog&version=1.1.3&to=tibble" data-mini-rdoc="tibble::tibble">tibble</a></code> with 419 rows and 4 columns:<dl class="dl-horizontal">
 <dt>id</dt><dd>The identification label of the individuals.</dd>
 <dt>snp</dt><dd>The SNP label.</dd>
 <dt>counts</dt><dd>The number of read-counts that support the reference allele.</dd>
 <dt>size</dt><dd>The total number of read-counts at a given SNP.</dd>
</dl>

Format

GBS data from Shirasawa et al (2017) — snpdat

A <code><a rd-options='tibble' href='tibble'>tibble</a></code> with 419 rows and 4 columns:<dl class='dl-horizontal'>
 <dt>id</dt><dd>The identification label of the individuals.</dd>
 <dt>snp</dt><dd>The SNP label.</dd>
 <dt>counts</dt><dd>The number of read-counts that support the reference allele.</dd>
 <dt>size</dt><dd>The total number of read-counts at a given SNP.</dd>
</dl>

snpdat: GBS data from Shirasawa et al (2017)

Description

Usage

Arguments

Value

Format

References