README.md

In tomoyukif/GBScleanR: Error correction tool for noisy genotyping by sequencing (GBS) data

GBScelaneR

Error correction tool for genotype data derived from reduced representation sequencing(RRS).

Introduction

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 allele 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.

Prerequisites

You may need to install the latest versions of the following packages.

BiocManager::install("gdsfmt")
BiocManager::install("SeqArray")
install.packages("ggplot2")
install.packages("tidyr")
install.packages("expm")
install.packages("Rcpp")
install.packages("RcppParallel")

# To create the vignette of GBScleanR
install.packages("rmarkdown")
install.packages("knitr")
BiocManager::install("BiocStyle")

Installation

You can install GBScleanR from the Bioconductor repository with running the following code on an R console. Currently GBScleanR is listed in the developmental package repository of Bioconductor(https://doi.org/doi:10.18129/B9.bioc.GBScleanR). You need to set to use Bioc devel as shown below. On the other hand, GBScleanR on the GitHub repository provide you the latest package with some developmental functions. If you need the stable release version of the package, please install the one on Bioconductor.

From Bioconductor:

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

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

BiocManager::install("GBScleanR")

From GitHub:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

devtools::install_github("tomoyukif/GBScleanR", build_vignettes = TRUE)

For more information see vignette or run the following code on a R console.

browseVignettes(package = "GBScleanR")

Citations

"Furuta, T., Yamamoto, T., Ashikari, M., GBScleanR: robust genotyping error correction using a hidden Markov model with error pattern recognition. Genetics 2023; doi: 10.1093/genetics/iyad055

tomoyukif/GBScleanR documentation built on Oct. 31, 2024, 2:43 a.m.