polyfreqs: Bayesian Population Genomics in Autopolyploids

Implements a Gibbs sampling algorithm to perform Bayesian inference on biallelic SNP frequencies, genotypes and heterozygosity (observed and expected) in a population of autopolyploids.

Author
Paul Blischak [aut, cre]
Date of publication
2015-09-25 09:04:08
Maintainer
Paul Blischak <blischak.4@osu.edu>
License
GPL (>= 2)
Version
1.0.0
URLs

View on CRAN

Man pages

get_map_genotypes
Maximum _a posteriori_ (MAP) estmation of autopolyploid...
point_Hexp
Estimation of expected heterozygosity
point_Hobs
Estimation of observed heterozygosity
polyfreqs
Bayesian population genomics in autopolyploids
polyfreqs_pps
Posterior predictive model checks for polyfreqs
ref_reads
Reference reads matrix
simple_freqs
Point estimation of allele frequencies based on read counts
sim_reads
Simulation of sequencing read counts and genotypes
total_reads
Total reads matrix

Files in this package

polyfreqs
polyfreqs/inst
polyfreqs/inst/doc
polyfreqs/inst/doc/polyfreqs_Intro.Rmd
polyfreqs/inst/doc/polyfreqs_Intro.R
polyfreqs/inst/doc/polyfreqs_Intro.html
polyfreqs/src
polyfreqs/src/ref_read_pmf.cpp
polyfreqs/src/sample_p.cpp
polyfreqs/src/sample_g.cpp
polyfreqs/src/sim_ref_reads.cpp
polyfreqs/src/RcppExports.cpp
polyfreqs/NAMESPACE
polyfreqs/data
polyfreqs/data/ref_reads.rda
polyfreqs/data/total_reads.rda
polyfreqs/R
polyfreqs/R/simple_freqs.R
polyfreqs/R/point_Hobs.R
polyfreqs/R/data_desc.R
polyfreqs/R/print_g.R
polyfreqs/R/point_Hexp.R
polyfreqs/R/polyfreqs.R
polyfreqs/R/sim_reads.R
polyfreqs/R/RcppExports.R
polyfreqs/R/polyfreqs_pps.R
polyfreqs/R/get_map_genotypes.R
polyfreqs/vignettes
polyfreqs/vignettes/polyfreqs_Intro.Rmd
polyfreqs/README.md
polyfreqs/MD5
polyfreqs/build
polyfreqs/build/vignette.rds
polyfreqs/DESCRIPTION
polyfreqs/man
polyfreqs/man/polyfreqs.Rd
polyfreqs/man/total_reads.Rd
polyfreqs/man/simple_freqs.Rd
polyfreqs/man/polyfreqs_pps.Rd
polyfreqs/man/point_Hobs.Rd
polyfreqs/man/point_Hexp.Rd
polyfreqs/man/sim_reads.Rd
polyfreqs/man/ref_reads.Rd
polyfreqs/man/get_map_genotypes.Rd