get_parent_outprop: E-step for the parents.

Description Usage Arguments Author(s)

View source: R/RcppExports.R

Description

E-step for the parents.

Usage

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get_parent_outprop(pcounts, psize, ploidy, pgeno, d, eps, tau, out_prop,
  out_mean, out_disp)

Arguments

pcounts

The number of counts of the reference allele we observe in a parent.

psize

The total number of reads we observe in a parent.

ploidy

An integer. The ploidy of the species. This is assumed to be the same for each individual.

pgeno

The genotype of the parent.

d

Same as bias_val in obj_parent.

eps

Same as seq_error in obj_parent.

tau

Same as od_param in obj_parent.

out_prop

The proportion of points that are outliers. Defaults (quite arbitrarily) to 0.01.

out_mean

The mean of beta-binomial for the outlier distribution. Defaults to 0.5.

out_disp

The overdispersion parameter of the outlier distribution. Defaults to 1/3, which corresponds to a uniform distribution for the underlying beta when out_mean = 0.5.

Author(s)

David Gerard


dcgerard/updogAlpha documentation built on May 14, 2019, 3:10 a.m.