format_multidog

This function will allow you to have genotype estimates, maximum posterior
probability, and other values in the form of a matrix/array. If multiple
variable names are provided, the data are formatted as a 3-dimensional
array with the dimensions corresponding to (individuals, SNPs, variables).

Implements empirical Bayes approaches to genotype
polyploids from next generation sequencing data while
accounting for allele bias, overdispersion, and sequencing
error. The main functions are flexdog() and multidog(),
which allow the specification
of many different genotype distributions. 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 (2020) <doi:10.1093/bioinformatics/btz852> for details
on the implemented methods.

David Gerard

updog

Flexible Genotyping for Polyploids

format_multidog function

<dl><dt>x</dt>
<dd>The output of <code>multidog</code>.</dd>
<dt>varname</dt>
<dd>A character vector of the variable names whose values
populate the cells. These should be column names from <code>x$inddf</code>.</dd></dl>

Arguments

Author

Return arrayicized elements from the output of multidog. — format_multidog

<dl>

<dt>x</dt>
<dd>The output of <code>multidog</code>.</dd>


<dt>varname</dt>
<dd>A character vector of the variable names whose values
populate the cells. These should be column names from <code>x$inddf</code>.</dd>

</dl>

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

Description

Usage

Arguments

Author

Details