API for dmgatti/DOQTL
Genotyping and QTL Mapping in DO Mice
| Global functions | |
|---|---|
| DO_autosome_recomb_freq | Man page |
| DO_femaleX_recomb_freq | Man page |
| DO_maleX_recomb_freq | Man page |
| add.missing.F1s | Man page Source code |
| add.sig.thr | Man page Source code |
| add.slash | Man page Source code |
| addLog | Man page Source code |
| addLogVector | Man page Source code |
| align.samples.snps | Source code |
| assign.autosome.femaleX.cases | Man page Source code |
| assoc.map | Man page Source code |
| assoc.map.perms | Man page Source code |
| assoc.plot | Man page Source code |
| assoc.scan1 | Man page Source code |
| assoc.scan1.perms | Source code |
| assoc.scan2 | Man page Source code |
| autosome.femaleX.trans.probs | Man page Source code |
| batch.normalize | Man page Source code |
| bayesint | Man page Source code |
| calc.genoprob | Man page Source code |
| calc.genoprob.alleles | Man page Source code |
| calc.genoprob.intensity | Man page Source code |
| calc.genoprob2 | Source code |
| categorize.variants | Man page |
| cc.trans.probs | Man page Source code |
| check.alleles | Source code |
| check.args | Man page Man page Source code |
| check.do.coat.color | Source code |
| check.genotype | Source code |
| chr.skeletons | Man page Source code |
| cluster.strains | Man page Source code |
| coef.doqtl | Man page Source code |
| coefplot | Man page Source code |
| colSumsLog | Man page Source code Source code |
| condense.model.probs | Man page Source code |
| condense.sanger.snps | Man page Source code |
| convert.allele.calls | Man page Source code |
| convert.genes.to.GRanges | Man page Source code |
| convert.genotypes | Man page Source code |
| convert.pos.to.GRanges | Man page Source code |
| convert.pos.to.bp | Man page Source code |
| convert.variants.to.GRanges | Man page Source code |
| convert.variants.to.numeric | Man page Source code |
| create.Rdata.files | Man page Source code |
| create.genotype.states | Man page Source code |
| create.html.page | Man page Source code |
| do.colors | Man page |
| do.pca | Source code |
| do.states | Man page |
| do.trans.probs | Man page Source code |
| do2sanger | Man page Source code |
| do2sanger.helper | Man page Source code |
| dof1.trans.probs | Source code |
| dohap2sanger | Source code |
| dohap2sanger.internal | Source code |
| emission.probs.allele | Man page Source code |
| emission.probs.intensity | Man page Source code |
| emission.probs.intensity2 | Source code |
| emission_prob_from_r | Man page |
| estimate.cluster.params | Man page Source code |
| estimate.cluster.params2 | Source code |
| example.genes | Man page |
| example.pheno | Man page |
| example.qtl | Man page |
| example.snps | Man page |
| extract.raw.data | Man page Source code |
| fast.qtlrel | Man page Source code |
| femaleX.trans.probs | Man page |
| fill.in.snps | Man page Source code |
| filter.geno.probs | Man page Source code |
| filter.samples | Man page Source code |
| filter_smooth_allele | Man page |
| filter_smooth_intensity | Man page |
| find.overlapping.genes | Man page Source code |
| founder.F1.intensity.plot | Man page Source code |
| gene.plot | Man page Source code |
| generic.trans.probs | Man page Source code |
| genomic.points | Man page Source code |
| genoprob.helper | Source code |
| genoprobs2hapblocks | Source code |
| genotype.by.sample.barplot | Man page Source code |
| genotype.by.snp.barplot | Man page Source code |
| get.F1.trans.probs | Source code |
| get.additive | Man page Source code |
| get.chr.lengths | Man page Source code |
| get.diplotype2haplotype.matrix | Source code |
| get.do.states | Man page Source code |
| get.dominance | Man page Source code |
| get.founder.probs | Source code |
| get.full | Man page Source code |
| get.gene.locations | Source code |
| get.gene.name | Man page Source code |
| get.genotype | Source code |
| get.haplogroup | Source code |
| get.haplogroup.allele | Source code |
| get.haplogroup.intensity | Source code |
| get.machine.precision | Man page Source code Source code |
| get.max.geno | Man page Source code |
| get.mgi.features | Man page Source code |
| get.missense.snps | Source code |
| get.num.auto | Man page Source code |
| get.pattern.variants | Man page Source code |
| get.pgw | Man page Source code |
| get.sig.thr | Man page Source code |
| get.snp.details | Source code |
| get.snp.patterns | Source code |
| get.strains | Man page Source code |
| get.trans.probs | Man page Source code |
| get.variants | Man page Source code |
| get.vcf.strains | Man page Source code |
| haploprobs2hapblocks | Source code |
| hmm.allele | Man page Source code |
| hmm.intensity | Man page Source code |
| hmm.intensity2 | Source code |
| hs.trans.probs | Source code |
| html.report | Man page Source code |
| impute.genotypes | Man page Source code |
| impute.markers | Source code |
| initialize.hmm | Man page Source code |
| intensity.mean.covar.plot | Man page Source code |
| interpolate.markers | Man page Source code Source code |
| keep.do.founders | Source code |
| keep.homozygotes | Man page Source code |
| kinship.alleles | Man page Source code |
| kinship.probs | Man page Source code |
| kinship_from_r | Man page |
| maleX.trans.probs | Man page Source code |
| matrixeqtl.snps | Man page Source code |
| muga.snps.to.keep | Man page |
| normalize.batches | Man page Source code |
| num.recomb.plot | Man page Source code |
| parameter.update.alleles | Man page Source code |
| parameter.update.intensity | Man page Source code |
| parameter.update.intensity2 | Source code |
| permutations.qtl.LRS | Man page Source code |
| plot.doqtl | Man page Source code |
| plot.genoprobs | Man page Source code |
| plot.genoprobs.max | Source code |
| plot.genoprobs.probs | Source code |
| plot.haplogroups | Source code |
| plot.scanone.assoc | Source code |
| prsmth.plot | Man page Source code |
| pxg.plot | Man page Source code |
| qtl.LRS | Man page Source code |
| qtl.heatmap | Man page Source code |
| qtl.qtlrel | Man page Source code |
| qtl.simulate | Man page Source code |
| quantilenorm | Man page Source code |
| query.pubmed | Source code |
| rankZ | Man page Source code |
| read.muga.data | Source code |
| read.vcf | Man page Source code |
| read.vcf.colnames | Source code |
| read.vcf.indel | Source code |
| read.vcf.snp | Source code |
| read.vcf.sv | Source code |
| rowSumsLog | Man page Source code Source code |
| s1.assoc | Source code |
| scanone | Man page Source code |
| scanone.K | Source code |
| scanone.LOCO | Source code |
| scanone.assoc | Man page Source code |
| scanone.eqtl | Man page Source code |
| scanone.loco | Source code |
| scanone.noK | Source code |
| scanone.perm | Man page Source code |
| sdp.plot | Man page Source code |
| sex.predict | Man page Source code |
| snp.plot | Man page Source code |
| strip.quality.columns | Man page Source code |
| summarize.by.samples | Man page Source code |
| summarize.by.snps | Man page Source code |
| summarize.genotype.transitions | Man page Source code |
| synch.sample.IDs | Source code |
| synchronize.snps | Source code |
| tabulate.geno | Man page Source code |
| update_alleles_from_r | Man page |
| update_from_r | Man page |
| variant.plot | Man page Source code |
| viterbi_from_r | Man page |
| write.founder.genomes | Man page Source code |
| write.founder.genomes.from.haps | Man page Source code |
| write.genoprob.plots | Man page Source code |
| write.results | Man page Source code |
| write.unc.hap.file | Source code |
