Package: updog 2.1.5

David Gerard

updog: Flexible Genotyping for Polyploids

Implements empirical Bayes approaches to genotype polyploids from next generation sequencing data while accounting for allele bias, overdispersion, and sequencing error. The main functions are flexdog() and multidog(), which allow the specification of many different genotype distributions. Also provided are functions to simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as functions to calculate oracle genotyping error rates, oracle_mis(), and correlation with the true genotypes, oracle_cor(). These latter two functions are useful for read depth calculations. Run browseVignettes(package = "updog") in R for example usage. See Gerard et al. (2018) <doi:10.1534/genetics.118.301468> and Gerard and Ferrao (2020) <doi:10.1093/bioinformatics/btz852> for details on the implemented methods.

Authors:David Gerard [aut, cre]

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updog.pdf |updog.html
updog/json (API)
NEWS

# Install updog in R:
install.packages('updog', repos = c('https://polyploids.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/dcgerard/updog/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • snpdat - GBS data from Shirasawa et al
  • uitdewilligen - Subset of individuals and SNPs from Uitdewilligen et al (2013).

On CRAN:

26 exports 22 stars 2.40 score 47 dependencies 1 dependents 385 downloads

Last updated 7 months agofrom:13e6a7b202d74e969f2837d2eeb136767593dc4f

Exports:dbetabinomfilter_snpflexdogflexdog_fullformat_multidogget_q_arrayis.flexdogis.multidoglog_sum_explog_sum_exp_2multidogoracle_cororacle_cor_from_jointoracle_jointoracle_misoracle_mis_from_jointoracle_mis_vecoracle_mis_vec_from_jointoracle_plotpbetabinomplot_genoqbetabinomrbetabinomrflexdogrgenowem

Dependencies:assertthatclicodetoolscolorspacedigestdoFuturedoRNGfansifarverforeachfuturefuture.applyggplot2globalsgluegtableisobanditeratorslabelinglatticelifecyclelistenvmagrittrMASSMatrixmgcvmunsellnlmeparallellypillarpkgconfigplyrR6RColorBrewerRcppRcppArmadilloreshape2rlangrngtoolsscalesstringistringrtibbleutf8vctrsviridisLitewithr

Example Use of Updog

Rendered fromsmells_like_updog.Rmdusingknitr::rmarkdownon Jun 09 2024.

Last update: 2020-02-27
Started: 2018-05-04

Genotyping Many SNPs with multidog()

Rendered frommultidog.Rmdusingknitr::rmarkdownon Jun 09 2024.

Last update: 2023-11-15
Started: 2019-12-05

Oracle Calculations

Rendered fromoracle_calculations.Rmdusingknitr::rmarkdownon Jun 09 2024.

Last update: 2020-02-27
Started: 2018-05-11

Simulate Next-Generation Sequencing Data

Rendered fromsimulate_ngs.Rmdusingknitr::rmarkdownon Jun 09 2024.

Last update: 2020-02-27
Started: 2018-05-04

Readme and manuals

Help Manual

Help pageTopics
'updog' Flexible Genotyping for Polyploidsupdog-package updog
The Beta-Binomial Distributionbetabinom dbetabinom pbetabinom qbetabinom rbetabinom
Filter SNPs based on the output of 'multidog()'.filter_snp
Flexible genotyping for polyploids from next-generation sequencing data.flexdog
Flexible genotyping for polyploids from next-generation sequencing data.flexdog_full
Return arrayicized elements from the output of 'multidog'.format_multidog
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.get_q_array
Tests if an argument is a 'flexdog' object.is.flexdog
Tests if an argument is a 'multidog' object.is.multidog
Log-sum-exponential trick.log_sum_exp
Log-sum-exponential trick using just two doubles.log_sum_exp_2
Fit 'flexdog' to multiple SNPs.multidog
Calculates the correlation between the true genotype and an oracle estimator.oracle_cor
Calculate the correlation of the oracle estimator with the true genotype from the joint distribution matrix.oracle_cor_from_joint
The joint probability of the genotype and the genotype estimate of an oracle estimator.oracle_joint
Calculate oracle misclassification error rate.oracle_mis
Get the oracle misclassification error rate directly from the joint distribution of the genotype and the oracle estimator.oracle_mis_from_joint
Returns the oracle misclassification rates for each genotype.oracle_mis_vec
Get the oracle misclassification error rates (conditional on true genotype) directly from the joint distribution of the genotype and the oracle estimator.oracle_mis_vec_from_joint
Construct an oracle plot from the output of 'oracle_joint'.oracle_plot
Make a genotype plot.plot_geno
Draw a genotype plot from the output of 'flexdog'.plot.flexdog
Plot the output of 'multidog'.plot.multidog
Simulate GBS data from the 'flexdog' likelihood.rflexdog
Simulate individual genotypes from one of the supported 'flexdog' models.rgeno
GBS data from Shirasawa et al (2017)snpdat
Subset of individuals and SNPs from Uitdewilligen et al (2013).uitdewilligen
EM algorithm to fit weighted ash objective.wem