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GBScleanR

This is the development version of GBScleanR; for the stable release version, see GBScleanR.

Error correction tool for noisy genotyping by sequencing (GBS) data


Bioconductor version: Development (3.19)

GBScleanR is a package for quality check, filtering, and error correction of genotype data derived from next generation sequcener (NGS) based genotyping platforms. GBScleanR takes Variant Call Format (VCF) file as input. The main function of this package is `estGeno()` which estimates the true genotypes of samples from given read counts for genotype markers using a hidden Markov model with incorporating uneven observation ratio of allelic reads. This implementation gives robust genotype estimation even in noisy genotype data usually observed in Genotyping-By-Sequnencing (GBS) and similar methods, e.g. RADseq. The current implementation accepts genotype data of a diploid population at any generation of multi-parental cross, e.g. biparental F2 from inbred parents, biparental F2 from outbred parents, and 8-way recombinant inbred lines (8-way RILs) which can be refered to as MAGIC population.

Author: Tomoyuki Furuta [aut, cre]

Maintainer: Tomoyuki Furuta <f.tomoyuki at okayama-u.ac.jp>

Citation (from within R, enter citation("GBScleanR")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("GBScleanR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GBScleanR")
BasicUsageOfGBScleanR.html HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneticVariability, Genetics, HiddenMarkovModel, QualityControl, SNP, Sequencing, Software
Version 1.7.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3 + file LICENSE
Depends SeqArray
Imports stats, utils, methods, ggplot2, tidyr, expm, Rcpp, RcppParallel, gdsfmt
System Requirements GNU make, C++11
URL https://github.com/tomoyukif/GBScleanR
Bug Reports https://github.com/tomoyukif/GBScleanR/issues
See More
Suggests BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown
Linking To Rcpp, RcppParallel
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GBScleanR_1.7.0.tar.gz
Windows Binary GBScleanR_1.7.0.zip
macOS Binary (x86_64) GBScleanR_1.7.0.tgz
macOS Binary (arm64) GBScleanR_1.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GBScleanR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GBScleanR
Bioc Package Browser https://code.bioconductor.org/browse/GBScleanR/
Package Short Url https://bioconductor.org/packages/GBScleanR/
Package Downloads Report Download Stats