Man pages for vsbuffalo/ProgenyArray
Some statistical genetics for progeny array experiments
| alleleFreqs | Calculate allele frequenceies. |
| allSibFamilies | Get all sibling families for a ProgenyArray object |
| approxGeneticMap | This uses a monotonic polynomial regression (9th order by... |
| caclulateLODs | calculate LODs for QQ/UU and QU/UU, for maximum parent 1 and... |
| calcFreqs | Calculate allele frequencies |
| calcFreqs-ProgenyArray-method | Calculate allele frequencies from parents in a ProgenyArray |
| emHaplotypeImpute | Use EM Haplotype Phasing by Imputation Algorithm (internal... |
| emPlot | A diagnostic plot of haplotype imputation of simulated data |
| extractProgenyHaplotypes | Extract all progeny haplotypes from all parents |
| fathers | Accessor for fathers (returning indices or names) |
| fathers-ProgenyArray-method | Accessor for fathers in a ProgenyArray object |
| fathers-set | Setter for fathers |
| filterSibFamilies | Filter sibling families by minimum number of offspring |
| freqs | Getter for frequencies |
| freqs-ProgenyArray-method | Getter for allele frequencies |
| freqs-set | Setter for frequencies |
| geneticTiles | Create a PhasingTiles object for tiles based on genetic... |
| genotypeFreqs | Calculate genotype frequencies. |
| genotypingErrorMatrix | Create a genotyping error matrix. |
| granges-ProgenyArray-method | Accessor for genomic ranges from a ProgenyArray object |
| hapAgreementStats | Agreement Rate (across both haplotypes) for all windows |
| HW | Create dataframe of Hardy-Weinberg values. |
| HWPlot | Plot genotype and allele frequencies. |
| inferParents | Accessor for inferParents |
| inferParents-ProgenyArray-method | Infer parents of all progeny in a ProgenyArray |
| inferParents-SimulatedProgenyArray-method | Infer parents for SimulatedProgenyArray |
| isSelfed | Method to calculate if progeny is selfed |
| isSelfed-ProgenyArray-method | Method to check if individual is selfed |
| loadGeneticMap | Load genetic map of four columns: marker, chrom, position,... |
| lodcutoff | Getter for LOD cutoff |
| lodcutoff-set | Setter for LOD cutoff |
| MendelianTransmissionWithError | Create a Mendelian transmission matrix, with error in... |
| miMatrixPerTile | Trio Mendelian inconsistency across full-sib family per... |
| miRates | Mendelian inconsistency rates across a chromosome |
| mothers | Accessor for mothers (returning indices or names) |
| mothers-ProgenyArray-method | Accessor for mothers in a ProgenyArray object |
| mothers-set | Setter for mothers |
| parentage | Create parentage dataframe |
| parentGenotypes | Accessor for parentGenotypes |
| parentGenotypes-ProgenyArray-method | Accessor for parent genotypes |
| parentGenotypes-SimulatedProgenyArray-method | Accessor for parent genotypes |
| parentLLPlot | Create a diagnostic plot of a parentage inference, looking at... |
| parentLLPlot-ProgenyArray-method | Create a diagnostic plot of a parentage inference, looking at... |
| parentNames | Accessor for parents sample names |
| parentNames-ProgenyArray-method | Return parent sample names |
| parentNames-set | Setter for parents sample names |
| parents | Accessor for parents (returning indices or names) |
| parents-ProgenyArray-method | Accessor for parents 'data.frame' in a ProgenyArray object |
| phaseParents | Phase all parents data in a ProgenyArray |
| phaseParents-ProgenyArray-method | Phase all Parents in a ProgenyArray object |
| phases | Output all a simplified table of phasing data |
| phaseSibFamily | Phase Sibling Family by Haplotype Imputation |
| phases-ProgenyArray-method | Merge phasing data |
| PhasingTiles-class | A container for tiles used for phasing by imputation |
| physicalTiles | Create a PhasingTiles object for tiles based on physical... |
| plotGeneticMap | Function to inspect the Montonic Polynomial Regression... |
| predictGeneticMap | Use Monotonic Polynomial Regression Fits to Predict Genetic... |
| ProgenyArray | ProgenyArray. |
| ProgenyArray-class | An S4 class that stores genotyping data from a progeny array... |
| progenyArray-SimulatedProgenyArray-method | Accessor for ProgenyArray object |
| progenyGenotypes | Accessor for progenyGenotypes |
| progenyGenotypes-ProgenyArray-method | Accessor for progeny genotypes |
| progenyGenotypes-SimulatedProgenyArray-method | Accessor for progeny genotypes |
| progenyNames | Accessor for progeny sample names |
| progenyNames-ProgenyArray-method | Return progeny sample names |
| progenyNames-set | Setter for progeny sample names |
| show-PhasingTiles-method | Pretty-print a PhasingTiles object |
| show-ProgenyArray-method | Pretty-print a ProgenyArray object |
| sibFamily | Simulate a half-sib family, fixed number of sites |
| SimulatedProgenyArray | Create some simulation data |
| SimulatedProgenyArray-class | An S4 class that wraps a ProgenyArray object of noisy,... |
| snpTiles | Create a PhasingTiles object for tiles based on fixed number... |
| suppliedMothers | Accessor for user-supplied mothers (returning indices or... |
| suppliedMothers-ProgenyArray-method | Accessor for user-supplied mothers |
| suppliedMothers-set | Accessor for user-supplied mothers |
| tileRef | A function that gets the reference alleles used in the tiles.... |
| whichLociComplete | Return which loci are complete |
| whichLociPolymorphic | Which loci are not fixed |
| whichRowColMax | which.max for matrices |
