DOQTL

Package: DOQTL
Version: 1.8.0
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, doMPI
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
NeedsCompilation: yes
Packaged: 2016-05-04 05:39:30 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'DOQTL' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c DOrec.c -o DOrec.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c DOstep.c -o DOstep.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c DOstep_Rwrappers.c -o DOstep_Rwrappers.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c addlog.c -o addlog.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c emission_prob.c -o emission_prob.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c emission_prob2.c -o emission_prob2.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c filter.smooth.allele.c -o filter.smooth.allele.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c filter.smooth.intensity.c -o filter.smooth.intensity.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c kinship.c -o kinship.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ri4hap.c -o ri4hap.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c transition.c -o transition.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c update.alleles.c -o update.alleles.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c update.c -o update.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c viterbi.c -o viterbi.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o DOQTL.so DOrec.o DOstep.o DOstep_Rwrappers.o addlog.o emission_prob.o emission_prob2.o filter.smooth.allele.o filter.smooth.intensity.o init.o kinship.o ri4hap.o transition.o update.alleles.o update.o viterbi.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/DOQTL/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DOQTL'
    finding HTML links ... done
    add.missing.F1s                         html  
    add.sig.thr                             html  
    add.slash                               html  
    addLog                                  html  
    addLogVector                            html  
    assoc.map                               html  
    assoc.plot                              html  
    assoc.scan1                             html  
    assoc.scan2                             html  
    bayesint                                html  
    calc.genoprob                           html  
    calc.genoprob.alleles                   html  
    calc.genoprob.intensity                 html  
    categorize.variants                     html  
    cc.trans.probs                          html  
    cluster.strains                         html  
    coef.doqtl                              html  
    coefplot                                html  
    colSumsLog                              html  
    condense.model.probs                    html  
    condense.sanger.snps                    html  
    convert.allele.calls                    html  
    convert.genes.to.GRanges                html  
    convert.genotypes                       html  
    convert.variants.to.GRanges             html  
    convert.variants.to.numeric             html  
    create.Rdata.files                      html  
    create.genotype.states                  html  
    create.html.page                        html  
    do.colors                               html  
    do.states                               html  
    do.trans.probs                          html  
    do2sanger                               html  
    emission.probs.allele                   html  
    estimate.cluster.params                 html  
    example.genes                           html  
    example.pheno                           html  
    example.qtl                             html  
    example.snps                            html  
    extract.raw.data                        html  
    fast.qtlrel                             html  
    fill.in.snps                            html  
    filter.geno.probs                       html  
    filter.samples                          html  
    find.overlapping.genes                  html  
    gene.plot                               html  
    generic.trans.probs                     html  
    genome.plots                            html  
    genome.summary.plots                    html  
    get.chr.lengths                         html  
    get.do.states                           html  
    get.gene.name                           html  
    get.machine.precision                   html  
    get.max.geno                            html  
    get.mgi.features                        html  
    get.num.auto                            html  
    get.pattern.variants                    html  
    get.pgw                                 html  
    get.sig.thr                             html  
    get.strains                             html  
    get.trans.probs                         html  
    get.variants                            html  
    hmm                                     html  
    html.report                             html  
    impute.genotypes                        html  
    intensity.plots                         html  
    internal_functions                      html  
    interpolate.markers                     html  
    kinship                                 html  
    muga.snps.to.keep                       html  
    normalize.batches                       html  
    parameter.update                        html  
    plot.doqtl                              html  
    finding level-2 HTML links ... done

Rd warning: /tmp/RtmpIo6ZHk/R.INSTALL316cdfb8137/DOQTL/man/plot.doqtl.Rd:20: missing link 'get.sig.thr()'
    pxg.plot                                html  
    qtl.LRS                                 html  
    qtl.heatmap                             html  
    qtl.qtlrel                              html  
    qtl.simulate                            html  
    rankZ                                   html  
    read.vcf                                html  
    scanone                                 html  
    scanone.assoc                           html  
    scanone.eqtl                            html  
    scanone.perm                            html  
    sdp.plot                                html  
    sex.predict                             html  
    snp.plot                                html  
    summarize.genotype.transitions          html  
    update_from_r                           html  
    variant.plot                            html  
    write.founder.genomes                   html  
    write.results                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DOQTL)
Making 'packages.html' ... done