Man pages for updog
Flexible Genotyping for Polyploids
| betabinom | The Beta-Binomial Distribution |
| export_vcf | Save the output of 'multidog()' to a VCF file. |
| filter_snp | Filter SNPs based on the output of 'multidog()'. |
| flexdog | Flexible genotyping for polyploids from next-generation... |
| flexdog_full | Flexible genotyping for polyploids from next-generation... |
| format_multidog | Return arrayicized elements from the output of 'multidog'. |
| get_q_array | Return the probabilities of an offspring's genotype given its... |
| 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_cor_from_joint | Calculate the correlation of the oracle estimator with the... |
| oracle_joint | The joint probability of the genotype and the genotype... |
| oracle_mis | Calculate oracle misclassification error rate. |
| oracle_mis_from_joint | Get the oracle misclassification error rate directly from the... |
| oracle_mis_vec | Returns the oracle misclassification rates for each genotype. |
| oracle_mis_vec_from_joint | Get the oracle misclassification error rates (conditional on... |
| oracle_plot | Construct an oracle plot from the output of 'oracle_joint'. |
| plot.flexdog | Draw a genotype plot from the output of 'flexdog'. |
| plot_geno | Make a genotype plot. |
| plot.multidog | Plot the output of 'multidog'. |
| rflexdog | Simulate GBS data from the 'flexdog' likelihood. |
| rgeno | Simulate individual genotypes from one of the supported... |
| snpdat | GBS data from Shirasawa et al (2017) |
| uitdewilligen | Subset of individuals and SNPs from Uitdewilligen et al... |
| updog-package | 'updog' Flexible Genotyping for Polyploids |
| wem | EM algorithm to fit weighted ash objective. |
