Man pages for DOQTL
Genotyping and QTL Mapping in DO Mice
| 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. |
