get_out_prop: E step in EM algorithm for a single individual.

Description Usage Arguments Author(s)

View source: R/RcppExports.R

Description

E step in EM algorithm for a single individual.

Usage

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get_out_prop(ocounts, osize, ploidy, prob_geno, d, eps, tau, out_prop, out_mean,
  out_disp)

Arguments

ocounts

The observed counts of the refernce allele for each individual.

osize

The observed number of reads for each individuals.

ploidy

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

prob_geno

The allele frequencies of the genotypes. See get_prob_geno.

d

The sequencing bias parameter.

eps

The sequencing error rate

tau

The overdisperion parameter.

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.