DOQTL
This package is for version 3.6 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: 3.6
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("DOQTL")
):
Installation
To install this package, start R (version "3.4") 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 | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | GeneticVariability, Genetics, HiddenMarkovModel, SNP, Software |
Version | 1.14.0 |
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 |
See More
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_1.14.0.tar.gz |
Windows Binary | DOQTL_1.14.0.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | DOQTL_1.14.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/DOQTL |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DOQTL |
Package Short Url | https://bioconductor.org/packages/DOQTL/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.6 | Source Archive |