DOQTL: Genotyping and QTL Mapping in DO Mice

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
Date of publicationNone
MaintainerDaniel Gatti <Dan.Gatti@jax.org>
LicenseGPL-3
Version1.10.0
http://do.jax.org

View on Bioconductor

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.

Files in this package

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

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