updog: oracle_mis_from_joint – R documentation

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oracle_mis_from_joint

Get the oracle misclassification error rate directly from the joint distribution of the genotype and the oracle estimator.

Description

Get the oracle misclassification error rate directly from the joint distribution of the genotype and the oracle estimator.

Usage

oracle_mis_from_joint(jd)

Arguments

`jd`	A matrix of numerics. Element (i, j) is the probability of genotype i - 1 and estimated genotype j - 1. This is usually obtained from `oracle_joint`.

Value

A double. The oracle misclassification error rate.

Author(s)

David Gerard

References

Gerard, D., Ferrão, L. F. V., Garcia, A. A. F., & Stephens, M. (2018). Genotyping Polyploids from Messy Sequencing Data. Genetics, 210(3), 789-807. doi: 10.1534/genetics.118.301468.

Examples

## Hardy-Weinberg population with allele-frequency of 0.75.
## Moderate bias and moderate overdispersion.
ploidy <- 6
dist <- stats::dbinom(0:ploidy, ploidy, 0.75)
jd <- oracle_joint(n = 100, ploidy = ploidy, seq = 0.001,
                   bias = 0.7, od = 0.01, dist = dist)
oracle_mis_from_joint(jd = jd)

## Compare to oracle_cor
oracle_mis(n = 100, ploidy = ploidy, seq = 0.001,
           bias = 0.7, od = 0.01, dist = dist)

updog

Flexible Genotyping for Polyploids

v2.0.2

GPL-3

Authors

David Gerard [aut, cre] (<https://orcid.org/0000-0001-9450-5023>)

Initial release