Man pages for updog
Flexible Genotyping for Polyploids

betabinomThe Beta-Binomial Distribution
filter_snpFilter SNPs based on the output of 'multidog()'.
flexdogFlexible genotyping for polyploids from next-generation...
flexdog_fullFlexible genotyping for polyploids from next-generation...
format_multidogReturn arrayicized elements from the output of 'multidog'.
get_q_arrayReturn the probabilities of an offspring's genotype given its...
is.flexdogTests if an argument is a 'flexdog' object.
is.multidogTests if an argument is a 'multidog' object.
log_sum_expLog-sum-exponential trick.
log_sum_exp_2Log-sum-exponential trick using just two doubles.
multidogFit 'flexdog' to multiple SNPs.
oracle_corCalculates the correlation between the true genotype and an...
oracle_cor_from_jointCalculate the correlation of the oracle estimator with the...
oracle_jointThe joint probability of the genotype and the genotype...
oracle_misCalculate oracle misclassification error rate.
oracle_mis_from_jointGet the oracle misclassification error rate directly from the...
oracle_mis_vecReturns the oracle misclassification rates for each genotype.
oracle_mis_vec_from_jointGet the oracle misclassification error rates (conditional on...
oracle_plotConstruct an oracle plot from the output of 'oracle_joint'.
plot.flexdogDraw a genotype plot from the output of 'flexdog'.
plot_genoMake a genotype plot.
plot.multidogPlot the output of 'multidog'.
rflexdogSimulate GBS data from the 'flexdog' likelihood.
rgenoSimulate individual genotypes from one of the supported...
snpdatGBS data from Shirasawa et al (2017)
uitdewilligenSubset of individuals and SNPs from Uitdewilligen et al...
updog-package'updog' Flexible Genotyping for Polyploids
wemEM algorithm to fit weighted ash objective.
updog documentation built on Nov. 17, 2023, 9:06 a.m.