updog-package |
'updog' Flexible Genotyping for Polyploids |
betabinom |
The Beta-Binomial Distribution |
convolve_up |
Convolution between two discrete probability mass functions with support on 0:K. |
dbetabinom |
The Beta-Binomial Distribution |
flexdog |
Flexible genotyping for polyploids from next-generation sequencing data. |
flexdog_full |
Flexible genotyping for polyploids from next-generation sequencing data. |
format_multidog |
Return matricized elements from the output of 'multidog'. |
get_bivalent_probs |
Returns segregation probabilities, pairing representation and number of ref alleles given the ploidy. |
get_hyper_weights |
Return mixture weights needed to obtain a hypergeometric distribution. |
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. |
is.mupdog |
Tests if its argument is a mupdog 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 SNP's. |
mupdog |
Using correlation between individuals for genotyping. |
mupout |
A mupdog fit of the 'uitdewilligen' data. |
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.mupdog |
Draw a genotype plot from the output of 'mupdog'. |
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) |
summary.mupdog |
Provides some summaries from the output of 'mupdog'. |
uitdewilligen |
Subset of individuals and SNPs from Uitdewilligen et al (2013). |
updog |
'updog' Flexible Genotyping for Polyploids |
wem |
Generalized version of 'uni_em'. |