GBScleanR

DOI: 10.18129/B9.bioc.GBScleanR    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	BasicUsageOfGBScleanR.html
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneticVariability, Genetics, HiddenMarkovModel, QualityControl, SNP, Sequencing, Software
Version	1.0.6
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 years)
License	GPL-3 + file LICENSE
Depends	SeqArray
Imports	stats, utils, methods, ggplot2, tidyr, expm, Rcpp, RcppParallel, gdsfmt
LinkingTo	Rcpp, RcppParallel
Suggests	BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown
SystemRequirements	GNU make, C++11
Enhances
URL	https://github.com/tomoyukif/GBScleanR
BugReports	https://github.com/tomoyukif/GBScleanR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	GBScleanR_1.0.6.tar.gz
Windows Binary	GBScleanR_1.0.0.zip
macOS Binary (x86_64)	GBScleanR_1.0.6.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GBScleanR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GBScleanR
Package Short Url	https://bioconductor.org/packages/GBScleanR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.15	Source Archive