oracle_mis_from_joint: Get the oracle misclassification error rate directly from the...

In updog: Flexible Genotyping for Polyploids

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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1534/genetics.118.301468")}.

See Also

oracle_joint for getting jd. oracle_mis for not having to first calculate jd.

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 documentation built on May 29, 2024, 8:13 a.m.