Files in DOQTL

Genotyping and QTL Mapping in DO Mice

README.md inst/unitTests/test_qtl.R inst/unitTests/test_assoc.R inst/doc/QTL_Mapping_DO_Mice.R inst/doc/QTL_Mapping_DO_Mice.pdf inst/tutorial/Genotyping_DO_Mice.pdf inst/tutorial/Reading_MUGA_Data.pdf 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/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 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 tests/runTests.R