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updog

Flexible Genotyping for Polyploids

Implements empirical Bayes approaches to genotype polyploids from next generation sequencing data while accounting for allele bias, overdispersion, and sequencing error. The main functions are flexdog() and multidog(), which allow the specification of many different genotype distributions. Also provided are functions to simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as functions to calculate oracle genotyping error rates, oracle_mis(), and correlation with the true genotypes, oracle_cor(). These latter two functions are useful for read depth calculations. Run browseVignettes(package = "updog") in R for example usage. See Gerard et al. (2018) <doi:10.1534/genetics.118.301468> and Gerard and Ferrao (2020) <doi:10.1093/bioinformatics/btz852> for details on the implemented methods.

Functions (28)

betabinom

The Beta-Binomial Distribution

filter_snp

Filter SNPs based on the output of multidog().

flexdog

Flexible genotyping for polyploids from next-generation sequencing data.

flexdog_full

Flexible genotyping for polyploids from next-generation sequencing data.

format_multidog

Return arrayicized elements from the output of multidog.

get_q_array

Return the probabilities of an offspring's genotype given its parental genotypes for all possible combinations of parental and offspring genotypes. This is for species with polysomal inheritance and bivalent, non-preferential pairing.

is.flexdog

Tests if an argument is a flexdog object.

is.multidog

Tests if an argument is a multidog object.

log_sum_exp

Log-sum-exponential trick.

log_sum_exp_2

Log-sum-exponential trick using just two doubles.

multidog

Fit flexdog to multiple SNPs.

oracle_cor

Calculates the correlation between the true genotype and an oracle estimator.

oracle_cor_from_joint

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

oracle_joint

The joint probability of the genotype and the genotype estimate of an oracle estimator.

oracle_mis

Calculate oracle misclassification error rate.

oracle_mis_from_joint

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

oracle_mis_vec

Returns the oracle misclassification rates for each genotype.

oracle_mis_vec_from_joint

Get the oracle misclassification error rates (conditional on true genotype) directly from the joint distribution of the genotype and the oracle estimator.

oracle_plot

Construct an oracle plot from the output of oracle_joint.

plot.flexdog

Draw a genotype plot from the output of flexdog.

plot.multidog

Plot the output of multidog.

plot_geno

Make a genotype plot.

rflexdog

Simulate GBS data from the flexdog likelihood.

rgeno

Simulate individual genotypes from one of the supported flexdog models.