obj_offspring_weights: Same thing as 'obj_offspring', but each sample's log-density...

Description Usage Arguments Author(s)

View source: R/RcppExports.R

Description

This is mostly used in the EM algorithm.

Usage

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obj_offspring_weights(ocounts, osize, weight_vec, ploidy, prob_geno,
  bias_val = 1, seq_error = 0, od_param = 0, outlier = FALSE,
  out_prop = 0.01, out_mean = 0.5, out_disp = 1/3)

Arguments

ocounts

The observed counts of the refernce allele for each individual.

osize

The observed number of reads for each individuals.

weight_vec

A vector of numerics between 0 and 1. They don't have to sum to 1.

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.

bias_val

The bias parameter. A value of 1 means there is no bias toward one allele or the other. A value less than one indicates a bias toward the reference allele. A value greater than one indicates a bias toward the non-reference allele.

seq_error

The sequencing error rate.

od_param

The overdispersion parameter in the beta-binomial model for the OK counts. When this is zero, this resorts to the binomial model for counts.

outlier

A logical. Should we include an outlier model (TRUE) or not (FALSE)? Defaults to FALSE.

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.