API for 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 |
| add.sig.thr | Man page |
| add.slash | Man page |
| addLog | Man page |
| addLogVector | 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 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.GRanges | Man page |
| convert.pos.to.bp | Man page |
| convert.variants.to.GRanges | Man page |
| convert.variants.to.numeric | Man page |
| create.Rdata.files | Man page |
| create.genotype.states | Man page |
| create.html.page | Man page |
| do.colors | Man page |
| do.states | Man page |
| do.trans.probs | Man page |
| do2sanger | Man page |
| do2sanger.helper | Man page |
| emission.probs.allele | Man page |
| emission.probs.intensity | Man page |
| emission_prob_from_r | 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.do.states | Man page |
| get.dominance | 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.probs | Man page |
| kinship_from_r | 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.LRS | Man page |
| qtl.heatmap | 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 |
