DOQTL: Genotyping and QTL Mapping in DO Mice
Version 1.12.0

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.

AuthorDaniel Gatti, Karl Broman, Andrey Shabalin, Petr Simecek
Bioconductor views GeneticVariability Genetics HiddenMarkovModel SNP
Date of publicationNone
MaintainerDaniel Gatti <Dan.Gatti@jax.org>
LicenseGPL-3
Version1.12.0
URL http://do.jax.org
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DOQTL")

Getting started

README.md

Popular man pages

addLogVector: Add a vector of log values.
example.qtl: Example QTL.
fill.in.snps: Interpolate between SNPs at the same cM value.
filter.samples: FALSEilter X, Y and genotype data by call rate
get.num.auto: Get the number of autosomes
scanone.eqtl: Mapping using the Matrix EQTL algorithm.
update_from_r: Update parameters in HMM
See all...

All man pages Function index File listing

Man pages

addLog: Add two log values.
addLogVector: Add a vector of log values.
add.missing.F1s: Add Missing F1 Samples
add.sig.thr: Add the significance thresholds to an existing QTL plot.
add.slash: Add a forward slash to a character string.
assoc.map: Perform association mapping on DO mice.
assoc.plot: Plot association mapping results.
assoc.scan1: Scan one for association mapping.
assoc.scan2: Scan two for association mapping.
bayesint: Find a Bayesian Credible Interval around a QTL.
calc.genoprob: Calculate the founder genotype probabilities at each SNP.
calc.genoprob.alleles: Calculate the founder genotype probabilities at each SNP...
calc.genoprob.intensity: Calculate the founder genotype probabilities at each SNP.
categorize.variants: categorize.variants
cc.trans.probs: Transition probabilities for CC mice.
cluster.strains: cluster.strains
coef.doqtl: Return the coefficients of a DOQTL object.
coefplot: Plot the QTL model coefficients
colSumsLog: Sum columns of log transformed data.
condense.model.probs: Condense 36 state genotypes down to founder genotypes.
condense.sanger.snps: Create an HDF5 file with the unique SNP patterns between each...
convert.allele.calls: Convert allele calls to numeric values.
convert.genes.to.GRanges: Convert MGI genes to GRanges.
convert.genotypes: Convert the genotype data from A,C,G,T format to A, H, B, N.
convert.variants.to.GRanges: convert.variants.to.GRanges
convert.variants.to.numeric: convert.variants.to.numeric
create.genotype.states: Create genotype states.
create.html.page: Create an HTML QTL report
create.Rdata.files: Convert *.txt files to *.Rdata files.
do2sanger: Impute the Sanger SNPs onto DO genomes
do.colors: do.colors
do.states: do.states
do.trans.probs: Determine DO transition probabilities
emission.probs.allele: Calculate the emission probabilities
estimate.cluster.params: Estimate genotype cluster means and variances
example.genes: example.genes
example.pheno: Example phenotypes.
example.qtl: Example QTL.
example.snps: example.snps
extract.raw.data: Extract intensities, genotypes and call rates from from raw...
fast.qtlrel: QTL mapping using QTLRel
fill.in.snps: Interpolate between SNPs at the same cM value.
filter.geno.probs: Remove SNPs where the genotype probabilities are too low for...
filter.samples: FALSEilter X, Y and genotype data by call rate
find.overlapping.genes: find.overlapping.genes
gene.plot: gene.plot
generic.trans.probs: Generic transition probabilities
genome.plots: Plot the genome of a DO sample.
genome.summary.plots: Genome summary plots
get.chr.lengths: Get chromosome lengths for the mouse
get.do.states: Get the 36 genotype states for the DO
get.gene.name: Get the gene symbol
get.machine.precision: Get the machine precsion
get.max.geno: Get the genotype with the highest probability
get.mgi.features: get.mgi.features
get.num.auto: Get the number of autosomes
get.pattern.variants: get.pattern.variants
get.pgw: Get the genome wide p-value.
get.sig.thr: Get the significance thresholds.
get.strains: get.strains
get.trans.probs: Get the transition probabilities between markers.
get.variants: get.variants
hmm: HMM function.
html.report: Create an HTML report for a set of QTL
impute.genotypes: Impute Sanger SNPs onto mouse genomes.
intensity.plots: Plot founders and F1 hybrids or genotype state means and...
internal_functions: Internal functions for DOQTL
interpolate.markers: interpolate haplotype or genotype probabilities from one set...
kinship: Create a kinship matrix.
muga.snps.to.keep: SNPs to use for genotyping and mapping on the MUGA
normalize.batches: Batch normalize the X & Y intensity data.
parameter.update: Parameter updating in HMM
plot.doqtl: Plot a QTL
pxg.plot: Phenotype by genotype plot at a single marker.
qtl.heatmap: Plot a Heatmap of all QTL
qtl.LRS: QTL mapping with no kinship.
qtl.qtlrel: Use QTLRel to map a set of traits
qtl.simulate: Simulate a QTL in the DO
rankZ: Rank Z transformation
read.vcf: Read and parse VCF data
scanone: Perform a genome scan.
scanone.assoc: Map the entire genome using association mapping.
scanone.eqtl: Mapping using the Matrix EQTL algorithm.
scanone.perm: Perform a genome scan.
sdp.plot: Plot association mapping results.
sex.predict: Determine the sex of each sample
snp.plot: snp.plot
summarize.genotype.transitions: Summarize the genotype data output by the genotyping HMM.
update_from_r: Update parameters in HMM
variant.plot: variant.plot
write.founder.genomes: Write out the genotypes of DO samples
write.results: Write out HMM results.

Functions

DO_autosome_recomb_freq Man page
DO_femaleX_recomb_freq Man page
DO_maleX_recomb_freq Man page
add.missing.F1s Man page Source code
add.sig.thr Man page Source code
add.slash Man page Source code
addLog Man page Source code
addLogVector Man page Source code
align.samples.snps Source code
assign.autosome.femaleX.cases Man page Source code
assoc.map Man page Source code
assoc.map.perms Man page Source code
assoc.plot Man page Source code
assoc.scan1 Man page Source code
assoc.scan1.perms Source code
assoc.scan2 Man page Source code
autosome.femaleX.trans.probs Man page Source code
batch.normalize Man page Source code
bayesint Man page Source code
calc.genoprob Man page Source code
calc.genoprob.alleles Man page Source code
calc.genoprob.intensity Man page Source code
calc.genoprob2 Source code
categorize.variants Man page Source code
cc.trans.probs Man page Source code
check.alleles Source code
check.args Man page Man page Source code
check.do.coat.color Source code
check.genotype Source code
chr.skeletons Man page Source code
cluster.strains Man page Source code
coef.doqtl Man page Source code
coefplot Man page Source code
colSumsLog Man page Source code Source code
condense.model.probs Man page Source code
condense.sanger.snps Man page Source code
convert.allele.calls Man page Source code
convert.genes.to.GRanges Man page Source code
convert.genotypes Man page Source code
convert.pos.to.GRanges Man page Source code
convert.pos.to.bp Man page Source code
convert.variants.to.GRanges Man page Source code
convert.variants.to.numeric Man page Source code
create.Rdata.files Man page Source code
create.genotype.states Man page Source code
create.html.page Man page Source code
do.colors Man page
do.pca Source code
do.states Man page
do.trans.probs Man page Source code
do2sanger Man page Source code
do2sanger.helper Man page Source code
dof1.trans.probs Source code
dohap2sanger Source code
dohap2sanger.internal Source code
emission.probs.allele Man page Source code
emission.probs.intensity Man page Source code
emission.probs.intensity2 Source code
emission_prob_from_r Man page
estimate.cluster.params Man page Source code
estimate.cluster.params2 Source code
example.genes Man page
example.pheno Man page
example.qtl Man page
example.snps Man page
extract.raw.data Man page Source code
fast.qtlrel Man page Source code
femaleX.trans.probs Man page
fill.in.snps Man page Source code
filter.geno.probs Man page Source code
filter.samples Man page Source code
filter_smooth_allele Man page
filter_smooth_intensity Man page
find.overlapping.genes Man page Source code
founder.F1.intensity.plot Man page Source code
gene.plot Man page Source code
generic.trans.probs Man page Source code
genomic.points Man page Source code
genoprob.helper Source code
genoprobs2hapblocks Source code
genotype.by.sample.barplot Man page Source code
genotype.by.snp.barplot Man page Source code
get.F1.trans.probs Source code
get.additive Man page Source code
get.chr.lengths Man page Source code
get.diplotype2haplotype.matrix Source code
get.do.states Man page Source code
get.dominance Man page Source code
get.founder.probs Source code
get.full Man page Source code
get.gene.locations Source code
get.gene.name Man page Source code
get.genotype Source code
get.haplogroup Source code
get.haplogroup.allele Source code
get.haplogroup.intensity Source code
get.machine.precision Man page Source code Source code
get.max.geno Man page Source code
get.mgi.features Man page Source code
get.num.auto Man page Source code
get.pattern.variants Man page Source code
get.pgw Man page Source code
get.sig.thr Man page Source code
get.snp.details Source code
get.snp.patterns Source code
get.strains Man page Source code
get.trans.probs Man page Source code
get.variants Man page Source code
get.vcf.strains Man page Source code
haploprobs2hapblocks Source code
hmm.allele Man page Source code
hmm.intensity Man page Source code
hmm.intensity2 Source code
hs.trans.probs Source code
html.report Man page Source code
impute.genotypes Man page Source code
impute.markers Source code
initialize.hmm Man page Source code
intensity.mean.covar.plot Man page Source code
interpolate.markers Man page Source code Source code
keep.do.founders Source code
keep.homozygotes Man page Source code
kinship.alleles Man page Source code
kinship.probs Man page Source code
kinship_from_r Man page
maleX.trans.probs Man page Source code
matrixeqtl.snps Man page Source code
muga.snps.to.keep Man page
normalize.batches Man page Source code
num.recomb.plot Man page Source code
parameter.update.alleles Man page Source code
parameter.update.intensity Man page Source code
parameter.update.intensity2 Source code
permutations.qtl.LRS Man page Source code
plot.doqtl Man page Source code
plot.genoprobs Man page Source code
plot.genoprobs.max Source code
plot.genoprobs.probs Source code
plot.haplogroups Source code
plot.scanone.assoc Source code
prsmth.plot Man page Source code
pxg.plot Man page Source code
qtl.LRS Man page Source code
qtl.heatmap Man page Source code
qtl.qtlrel Man page Source code
qtl.simulate Man page Source code
quantilenorm Man page Source code
query.pubmed Source code
rankZ Man page Source code
read.muga.data Source code
read.vcf Man page Source code
read.vcf.colnames Source code
read.vcf.indel Source code
read.vcf.snp Source code
read.vcf.sv Source code
rowSumsLog Man page Source code Source code
s1.assoc Source code
scanone Man page Source code
scanone.K Source code
scanone.LOCO Source code
scanone.assoc Man page Source code
scanone.eqtl Man page Source code
scanone.loco Source code
scanone.noK Source code
scanone.perm Man page Source code
sdp.plot Man page Source code
sex.predict Man page Source code
snp.plot Man page Source code
strip.quality.columns Man page Source code
summarize.by.samples Man page Source code
summarize.by.snps Man page Source code
summarize.genotype.transitions Man page Source code
synch.sample.IDs Source code
synchronize.snps Source code
tabulate.geno Man page Source code
update_alleles_from_r Man page
update_from_r Man page
variant.plot Man page Source code
viterbi Source code
viterbi.allele Source code
viterbi.intensity Source code
viterbi_from_r Man page
write.founder.genomes Man page Source code
write.founder.genomes.from.haps Man page Source code
write.genoprob.plots Man page Source code
write.results Man page Source code
write.unc.hap.file Source code

Files

DESCRIPTION
NAMESPACE
R
R/add.missing.F1s.R
R/add.sig.thr.R
R/add.slash.R
R/addLog.R
R/align.samples.snps.R
R/assoc.map.R
R/bayesint.R
R/calc.genoprob.R
R/calc.genoprob.alleles.R
R/calc.genoprob.intensity.R
R/calc.genoprob2.R
R/categorize.variants.R
R/check.args.R
R/check.do.coat.color.R
R/cluster.strains.R
R/coef.doqtl.R
R/colSumsLog.R
R/condense.model.probs.R
R/condense.sanger.snps.R
R/convert.allele.calls.R
R/convert.genes.to.GRanges.R
R/convert.genotypes.R
R/convert.pos.to.GRanges.R
R/convert.variants.to.GRanges.R
R/convert.variants.to.numeric.R
R/create.Rdata.files.R
R/create.genotype.states.R
R/do2sanger.R
R/emission.probs.allele.R
R/emission.probs.intensity.R
R/estimate.cluster.params.R
R/extract.raw.data.R
R/fast.qtlrel.R
R/fill.in.snps.R
R/filter.geno.probs.R
R/filter.samples.R
R/find.overlapping.genes.R
R/gene.plot.R
R/genoprobs2hapblocks.R
R/genotype.plots.R
R/get.genotype.R
R/get.haplogroup.R
R/get.machine.precision.R
R/get.max.geno.R
R/get.mgi.features.R
R/get.pattern.variants.R
R/get.pgw.R
R/get.sig.thr.R
R/get.snp.details.R
R/get.strains.R
R/get.variants.R
R/hmm.allele.R
R/hmm.intensity.R
R/hmm.plotting.R
R/html.report.R
R/impute.genotypes.R
R/impute.markers.R
R/initialize.hmm.R
R/interploate.markers.R
R/interpolate.markers.R
R/kinship.R
R/normalize.batches.R
R/qtl.LRS.R
R/qtl.heatmap.R
R/qtl.plot.R
R/qtl.qtlrel.R
R/qtl.simulate.R
R/query.pubmed.R
R/rankZ.R
R/read.vcf.R
R/rowSumsLog.R
R/scanone.R
R/scanone.assoc.R
R/scanone.eqtl.R
R/scanone.perm.R
R/sex.predict.R
R/strip.quality.columns.R
R/summarize.genotype.data.R
R/sysdata.rda
R/transition.probs.R
R/update.parameters.R
R/utilities.R
R/variant.plot.R
R/viterbi.R
R/write.founder.genomes.R
R/write.results.R
README.md
build
build/vignette.rds
data
data/datalist
data/do.colors.rda
data/do.states.rda
data/example.genes.rda
data/example.pheno.rda
data/example.qtl.rda
data/example.snps.rda
data/hs.colors.rda
data/hsrat.colors.rda
data/muga.snps.to.keep.rda
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/QTL_Mapping_DO_Mice.R
inst/doc/QTL_Mapping_DO_Mice.Rnw
inst/doc/QTL_Mapping_DO_Mice.pdf
inst/tutorial
inst/tutorial/Genotyping_DO_Mice.Rnw
inst/tutorial/Genotyping_DO_Mice.pdf
inst/tutorial/Reading_MUGA_Data.Rnw
inst/tutorial/Reading_MUGA_Data.pdf
inst/unitTests
inst/unitTests/test_assoc.R
inst/unitTests/test_qtl.R
man
man/add.missing.F1s.Rd
man/add.sig.thr.Rd
man/add.slash.Rd
man/addLog.Rd
man/addLogVector.Rd
man/assoc.map.Rd
man/assoc.plot.Rd
man/assoc.scan1.Rd
man/assoc.scan2.Rd
man/bayesint.Rd
man/calc.genoprob.Rd
man/calc.genoprob.alleles.Rd
man/calc.genoprob.intensity.Rd
man/categorize.variants.Rd
man/cc.trans.probs.Rd
man/cluster.strains.Rd
man/coef.doqtl.Rd
man/coefplot.Rd
man/colSumsLog.Rd
man/condense.model.probs.Rd
man/condense.sanger.snps.Rd
man/convert.allele.calls.Rd
man/convert.genes.to.GRanges.Rd
man/convert.genotypes.Rd
man/convert.variants.to.GRanges.Rd
man/convert.variants.to.numeric.Rd
man/create.Rdata.files.Rd
man/create.genotype.states.Rd
man/create.html.page.Rd
man/do.colors.Rd
man/do.states.Rd
man/do.trans.probs.Rd
man/do2sanger.Rd
man/emission.probs.allele.Rd
man/estimate.cluster.params.Rd
man/example.genes.Rd
man/example.pheno.Rd
man/example.qtl.Rd
man/example.snps.Rd
man/extract.raw.data.Rd
man/fast.qtlrel.Rd
man/fill.in.snps.Rd
man/filter.geno.probs.Rd
man/filter.samples.Rd
man/find.overlapping.genes.Rd
man/gene.plot.Rd
man/generic.trans.probs.Rd
man/genome.plots.Rd
man/genome.summary.plots.Rd
man/get.chr.lengths.Rd
man/get.do.states.Rd
man/get.gene.name.Rd
man/get.machine.precision.Rd
man/get.max.geno.Rd
man/get.mgi.features.Rd
man/get.num.auto.Rd
man/get.pattern.variants.Rd
man/get.pgw.Rd
man/get.sig.thr.Rd
man/get.strains.Rd
man/get.trans.probs.Rd
man/get.variants.Rd
man/hmm.Rd
man/html.report.Rd
man/impute.genotypes.Rd
man/intensity.plots.Rd
man/internal_functions.Rd
man/interpolate.markers.Rd
man/kinship.Rd
man/muga.snps.to.keep.Rd
man/normalize.batches.Rd
man/parameter.update.Rd
man/plot.doqtl.Rd
man/pxg.plot.Rd
man/qtl.LRS.Rd
man/qtl.heatmap.Rd
man/qtl.qtlrel.Rd
man/qtl.simulate.Rd
man/rankZ.Rd
man/read.vcf.Rd
man/scanone.Rd
man/scanone.assoc.Rd
man/scanone.eqtl.Rd
man/scanone.perm.Rd
man/sdp.plot.Rd
man/sex.predict.Rd
man/snp.plot.Rd
man/summarize.genotype.transitions.Rd
man/update_from_r.Rd
man/variant.plot.Rd
man/write.founder.genomes.Rd
man/write.results.Rd
src
src/DOrec.c
src/DOstep.c
src/DOstep.h
src/DOstep_Rwrappers.c
src/DOstep_Rwrappers.h
src/addlog.c
src/addlog.h
src/emission_prob.c
src/emission_prob2.c
src/filter.smooth.allele.c
src/filter.smooth.intensity.c
src/init.c
src/init.h
src/kinship.c
src/ri4hap.c
src/transition.c
src/update.alleles.c
src/update.c
src/viterbi.c
tests
tests/runTests.R
vignettes
vignettes/QTL_Mapping_DO_Mice.Rnw
DOQTL documentation built on May 20, 2017, 10 p.m.

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