To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DOQTL")

In most cases, you don't need to download the package archive at all.

DOQTL

   

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see DOQTL.

Genotyping and QTL Mapping in DO Mice

Bioconductor version: 3.2

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

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

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DOQTL")

Documentation

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

browseVignettes("DOQTL")

 

PDF QTL Mapping using Diversity Outbred Mice
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneticVariability, Genetics, HiddenMarkovModel, SNP, Software
Version 1.6.0
In Bioconductor since BioC 3.0 (R-3.1) (1.5 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
LinkingTo
Suggests MUGAExampleData, doMPI
SystemRequirements
Enhances
URL http://do.jax.org
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source DOQTL_1.6.0.tar.gz
Windows Binary DOQTL_1.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) DOQTL_1.6.0.tgz
Mac OS X 10.9 (Mavericks) DOQTL_1.6.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/DOQTL/tree/release-3.2
Package Short Url http://bioconductor.org/packages/DOQTL/
Package Downloads Report Download Stats

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