doutdist

<p>Return the log density <code>TRUE</code> or not <code>FALSE</code>?</p>

logp

<p>The outlier distribution we use. Right now it is just a
beta binomial with mean 1/2 and od 1/3 (so underlying beta
is just a uniform from 0 to 1).</p>

internal

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

doutdist function

The outlier distribution we use. Right now it is just a
beta binomial with mean 1/2 and od 1/3 (so underlying beta
is just a uniform from 0 to 1). — doutdist

doutdist: The outlier distribution we use. Right now it is just a beta binomial with mean 1/2 and od 1/3 (so underlying beta is just a uniform from 0 to 1).

Description

Usage

Arguments

Value