DOQTL

This package is for version 3.7 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: 3.7

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 "3.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneticVariability, Genetics, HiddenMarkovModel, SNP, Software
Version	1.16.2
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

Suggests	MUGAExampleData, doMPI
Linking To
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	DOQTL_1.16.2.tar.gz
Windows Binary	DOQTL_1.16.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	DOQTL_1.16.2.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 3.7	Source Archive