plot.multidog

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

A vector of integers. The indices of the SNP's to plot.

indices

Produce genotype plots 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>. You may
select which SNP's to plot.

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

plot.multidog function

The output of <code><a rd-options='' href='multidog'>multidog</a></code>.

Produce genotype plots from the output of <code><a rd-options='' href='multidog'>multidog</a></code>. You may
select which SNP's to plot.

plot.multidog: Plot the output of `multidog`.

Description

Usage

Arguments

See Also