Read depth data from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian probability estimates of genotypes in polyploids or diploids. The genotype probabilities, posterior mean genotypes, or most probable genotypes can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2019) <doi:10.1534/g3.118.200913>, and the Hind/He statistic for marker filtering is described by Clark et al. (2022) <doi:10.1186/s12859-022-04635-9>. A variant calling pipeline for highly duplicated genomes is also included and is described by Clark et al. (2020, Version 1) <doi:10.1101/2020.01.11.902890>.
Version: 2.0.0 Depends: R (≥ 3.5.0), methods Imports: fastmatch, pcaMethods, Rcpp, stringi LinkingTo: Rcpp Suggests: rrBLUP, Rsamtools, GenomeInfoDb, Biostrings, GenomicRanges, VariantAnnotation, SummarizedExperiment, S4Vectors, IRanges, BiocGenerics, knitr, rmarkdown, GenomicFeatures, ggplot2, adegenet Published: 2022-11-06 DOI: 10.32614/CRAN.package.polyRAD Author: Lindsay V. Clark [aut, cre], U.S. National Science Foundation [fnd] Maintainer: Lindsay V. Clark <Lindsay.Clark at seattlechildrens.org> License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] URL: https://github.com/lvclark/polyRAD NeedsCompilation: yes Citation: polyRAD citation info Materials: NEWS CRAN checks: polyRAD results Documentation: Downloads: Reverse dependencies: Linking:Please use the canonical form https://CRAN.R-project.org/package=polyRAD to link to this page.
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