oracle_cor_from_joint {updog}

Calculate the correlation of the oracle estimator with the true genotype from the joint distribution matrix.

Description

Calculates the correlation between the oracle MAP estimator (where we have perfect knowledge about the data generation process) and the true genotype. This is a useful approximation when you have a lot of individuals.

Usage

oracle_cor_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

The Pearson correlation between the true genotype and the oracle estimator.

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.

See Also

oracle_joint for getting jd. oracle_cor 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_cor_from_joint(jd = jd)

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