pivec_from_segmats

The matrix of segregation probabilities for each
component for parent 1. The rows index the components and the
columns index the number of alleles to segregate.

p1segmat

The matrix of segregation probabilities for each
component for parent 2. The rows index the components and the
columns index the number of alleles to segregate.

p2segmat

A vector of weights for each component (row) of
<code>p1segmat</code>.

p1weight

A vector of weights for each component (row) of
<code>p2segmat</code>.

p2weight

Function to get the segregation probabilities from the distributions
of each component and the weights of each component.

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.

pivec_from_segmats: Function to get the segregation probabilities from the distributions of each component and the weights of each component.

Description

Usage

Arguments

Value

See Also