bbmix: Bayesian Model for Genotyping using RNA-Seq

Package: bbmix 1.0.0

bbmix: Bayesian Model for Genotyping using RNA-Seq

The method models RNA-seq reads using a mixture of 3 beta-binomial distributions to generate posterior probabilities for genotyping bi-allelic single nucleotide polymorphisms. Elena Vigorito, Anne Barton, Costantino Pitzalis, Myles J. Lewis and Chris Wallace (2023) <doi:10.1093/bioinformatics/btad393> "BBmix: a Bayesian beta-binomial mixture model for accurate genotyping from RNA-sequencing."

Authors:Elena Vigorito [aut, cre], Chris Wallace [aut]

bbmix_1.0.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
bbmix/json (API)

# Install 'bbmix' in R:

install.packages('bbmix', repos = c('https://evigorito.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

2.70 score 328 downloads 4 exports 53 dependencies

Last updated from:ef559b819b. Checks:12 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	229
linux-devel-x86_64	OK	238
source / vignettes	OK	298
linux-release-arm64	OK	246
linux-release-x86_64	OK	274
macos-release-arm64	OK	148
macos-release-x86_64	OK	489
macos-oldrel-arm64	OK	199
macos-oldrel-x86_64	OK	483
windows-devel	OK	265
windows-release	OK	270
windows-oldrel	OK	269
wasm-release	FAIL	190

Exports:call_gt ex_alt_hom fit_bb poolreads

Dependencies:abind backports BH callr checkmate cli cpp11 data.table desc distributional farver generics ggplot2 glue gridExtra gtable inline isoband labeling lifecycle loo magrittr matrixStats numDeriv otel pillar pkgbuild pkgconfig posterior processx ps QuickJSR R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppEigen RcppParallel rlang rmutil rstan rstantools S7 scales StanHeaders tensorA tibble utf8 vctrs viridisLite withr

BBmix: genotyping using RNA-seq

Rendered frombbmix.Rmdusingknitr::rmarkdown

Help page	Topics
The 'bbmix' package.	bbmix-package bbmix
Call genotypes using beta binomial after model training	call_gt
call gt helper, calculate mean dbetabinom from all posterior samples	call_help
Exclude fSNPs with no alternative allele in any sample. Also exclude fSNPs if all samples are hom.	ex_alt_hom
Fit beta binomial distribution to allelic counts for homozygous reference, heterozygous, homozygous alternative	fit_bb
call gt helper, get posterior mean, expected gt and sd expected gt across all samples	gt_help
Pool randomly selected reads from different files	poolreads

Help page

Topics

The 'bbmix' package.

bbmix-package bbmix

Call genotypes using beta binomial after model training

call_gt

call gt helper, calculate mean dbetabinom from all posterior samples

call_help

Exclude fSNPs with no alternative allele in any sample. Also exclude fSNPs if all samples are hom.

ex_alt_hom

Fit beta binomial distribution to allelic counts for homozygous reference, heterozygous, homozygous alternative

fit_bb