Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

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, or genotypes sampled from those probabilties, can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2018) .


News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("polyRAD")

1.0 by Lindsay V. Clark, 3 months ago


https://github.com/lvclark/polyRAD


Browse source code at https://github.com/cran/polyRAD


Authors: Lindsay V. Clark [aut, cre] , U.S. National Science Foundation [fnd]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports fastmatch, pcaMethods, methods, Rcpp

Suggests rrBLUP, Rsamtools, GenomeInfoDb, Biostrings, GenomicRanges, VariantAnnotation, SummarizedExperiment, S4Vectors, IRanges, BiocGenerics, knitr, rmarkdown, GenomicFeatures, qqman

Linking to Rcpp


See at CRAN