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whoa
View on CRAN: Click
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Download and install whoa package within the R console
Install from CRAN:
install.packages("whoa")
Install from Github:
library("remotes")
install_github("cran/whoa")
Install by package version:
library("remotes")
install_version("whoa", "0.0.2")
Attach the package and use:
library("whoa")
Maintained by
Eric C. Anderson
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All associated links for this package
First Published: 2019-08-02
Latest Update: 2021-08-11
Description:
This is a small, lightweight package that lets users investigate the distribution of genotypes in genotype-by-sequencing (GBS) data where they expect (by and large) Hardy-Weinberg equilibrium, in order to assess rates of genotyping errors and the dependence of those rates on read depth.It implements a Markov chain Monte Carlo (MCMC) sampler using 'Rcpp' to compute a Bayesian estimate of what we call the heterozygote miscall rate for restriction-associated digest (RAD) sequencing data and other types of reduced representation GBS data. It also provides functions to generate plots of expected and observed genotype frequencies. Some background on these topics can be found in a recent paper "Recent advances in conservation and population genomics data analysis" by Hendricks et al. (2018) <doi:10.1111/eva.12659>, and another paper describing the MCMC approach is in preparation with Gordon Luikart and Thierry Gosselin.
How to cite:
Eric C. Anderson (2019). whoa: Evaluation of Genotyping Error in Genotype-by-Sequencing Data. R package version 0.0.2, https://cran.r-project.org/web/packages/whoa. Accessed 21 Nov. 2024.
Previous versions and publish date:
0.0.1 (2019-08-02 13:20)
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Complete documentation for whoa
Functions, R codes and Examples using
the whoa R package
Some associated functions: bin_depths . estimate_m_rd . exp_and_obs_geno_freqs . geno_freq_boundaries . geno_freq_calc_single . geno_freqs_scatter . gibbsM . gibbsP . gibbsX . infer_m . lobster_buz_2000 . lobster_buz_2000_as_012_matrix . make_it_012 . posteriors_plot . prep_vcf_for_est_m_rd . tidy_m_ests . whoa .
Some associated R codes: RcppExports.R . bin_depths.R . data.R . exp_and_obs_geno_freqs.R . geno_freq_boundaries.R . geno_freq_count_single.R . geno_freqs_scatter.R . infer_m.R . posteriors_plot.R . prep_vcf_for_est_m_rd.R . tidy_m_ests.R . whoa.R . Full whoa package functions and examples
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