uitdewilligen

A list containing a matrix of reference counts, a matrix of total counts, and the ploidy level (4) of the species.
This is a subset of the data from Uitdewilligen et al (2013).

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

uitdewilligen function

A list containing three objects. Two matrices and a numeric scalar:<dl class="dl-horizontal">
 <dt>refmat</dt><dd>A matrix of read counts containing the reference allele. The rows index the individuals and the columns index the SNPs.</dd>
 <dt>sizemat</dt><dd>A matrix of the total number of read counts. The rows index the individuals and the columns index the SNPs.</dd>
 <dt>ploidy</dt><dd>The ploidy level of the species (just 4).</dd>
</dl>

Format

Subset of individuals and SNPs from Uitdewilligen et al (2013). — uitdewilligen

A list containing three objects. Two matrices and a numeric scalar:<dl class='dl-horizontal'>
 <dt>refmat</dt><dd>A matrix of read counts containing the reference allele. The rows index the individuals and the columns index the SNPs.</dd>
 <dt>sizemat</dt><dd>A matrix of the total number of read counts. The rows index the individuals and the columns index the SNPs.</dd>
 <dt>ploidy</dt><dd>The ploidy level of the species (just 4).</dd>
</dl>

uitdewilligen: Subset of individuals and SNPs from Uitdewilligen et al (2013).

Description

Usage

Arguments

Value

Format

References

See Also