format_multidog

The output of <code>multidog</code>.

The variable whose values populate the cells. This should
be a single columne from <code>x$inddf</code>.

varname

This function will allow you to have genotype estimates, maximum posterior
probability, and other values in the form of a matrix.

Implements empirical Bayes approaches to genotype
polyploids from next generation sequencing data while
accounting for allelic bias, overdispersion, and sequencing
error. The main functions are flexdog() and multidog(),
which allow 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

format_multidog function

Return matricized elements from the output of <code><a rd-options='' href='multidog'>multidog</a></code>. — format_multidog

Return matricized elements from the output of <code><a rd-options='' href='multidog'>multidog</a></code>.

Return matricized elements from the output of <code><a rd-options="" href="/link/multidog?package=updog&version=1.2.0" data-mini-rdoc="updog::multidog">multidog</a></code>.

format_multidog: Return matricized elements from the output of `multidog`.

Description

Usage

Arguments