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.

Author
Daniel Gatti, Karl Broman, Andrey Shabalin, Petr Simecek
Date of publication
None
Maintainer
Daniel Gatti <Dan.Gatti@jax.org>
License
GPL-3
Version
1.10.0
URLs

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