Function reference • updog

All functions

dbetabinom() pbetabinom() qbetabinom() rbetabinom(): 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.

snpdat: GBS data from Shirasawa et al (2017)

uitdewilligen: Subset of individuals and SNPs from Uitdewilligen et al (2013).

updog-package updog: updog Flexible Genotyping for Polyploids

wem(): EM algorithm to fit weighted ash objective.