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