Flexible Genotyping for Polyploids

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Documentation for package ‘updog’ version 2.1.5

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updog-package 'updog' Flexible Genotyping for Polyploids
betabinom The Beta-Binomial Distribution
dbetabinom 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'.
pbetabinom The Beta-Binomial Distribution
plot.flexdog Draw a genotype plot from the output of 'flexdog'.
plot.multidog Plot the output of 'multidog'.
plot_geno Make a genotype plot.
qbetabinom The Beta-Binomial Distribution
rbetabinom The Beta-Binomial Distribution
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 'updog' Flexible Genotyping for Polyploids
wem EM algorithm to fit weighted ash objective.