DOQTL

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see DOQTL.

Genotyping and QTL Mapping in DO Mice


Bioconductor version: 3.9

DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, DOQTL can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.

Author: Daniel Gatti, Karl Broman, Andrey Shabalin, Petr Simecek

Maintainer: Daniel Gatti <Dan.Gatti at jax.org>

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

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("DOQTL")

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("DOQTL")
QTL Mapping using Diversity Outbred Mice PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneticVariability, Genetics, HiddenMarkovModel, SNP, Software
Version 1.19.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL-3
Depends R (>= 3.0.0), BSgenome.Mmusculus.UCSC.mm10, GenomicRanges, VariantAnnotation
Imports annotate, annotationTools, biomaRt, Biobase, BiocGenerics, corpcor, doParallel, foreach, fpc, hwriter, IRanges, iterators, mclust, QTLRel, regress, rhdf5, Rsamtools, RUnit, XML
System Requirements
URL http://do.jax.org
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Suggests MUGAExampleData
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Package Archives

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

Source Package DOQTL_1.19.0.tar.gz
Windows Binary DOQTL_1.19.0.zip
Mac OS X 10.11 (El Capitan) DOQTL_1.19.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DOQTL
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DOQTL
Bioc Package Browser https://code.bioconductor.org/browse/DOQTL/
Package Short Url https://bioconductor.org/packages/DOQTL/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive