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.

Functions

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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