Get the oracle misclassification error rates (conditional on true genotype) directly from the joint distribution of the genotype and the oracle estimator.
Get the oracle misclassification error rates (conditional on true genotype) directly from the joint distribution of the genotype and the oracle estimator.
oracle_mis_vec_from_joint(jd)
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 |
A vector of numerics. Element i is the oracle misclassification error rate when genotyping an individual with actual genotype i + 1.
David Gerard
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.
oracle_joint for getting jd.
oracle_mis_vec for not having to first calculate
jd.
## 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_vec_from_joint(jd = jd)
## Compare to oracle_cor
oracle_mis_vec(n = 100, ploidy = ploidy, seq = 0.001,
bias = 0.7, od = 0.01, dist = dist)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.