DESCRIPTION

Package: DOQTL
Version: 1.17.5
Date: 2012-12-07
Title: Genotyping and QTL Mapping in DO Mice
Author: Daniel Gatti, Karl Broman, Andrey Shabalin, Petr Simecek
Maintainer: Daniel Gatti <Dan.Gatti@jax.org>
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
Suggests: MUGAExampleData
Description: 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.
biocViews: GeneticVariability, SNP, Genetics, HiddenMarkovModel
License: GPL-3
LazyData: true
ByteCompile: yes
URL: http://do.jax.org