Calculate the correlation of the oracle estimator with the true genotype from the joint distribution matrix.
Source:R/oracle.R
oracle_cor_from_joint.Rd
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.
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
.
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)
#> [1] 0.940216
## Compare to oracle_cor
oracle_cor(n = 100, ploidy = ploidy, seq = 0.001,
bias = 0.7, od = 0.01, dist = dist)
#> [1] 0.940216