Man pages for hsphase
Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data
| addSwitch | Add Switches |
| aio | All-in-one Phasing |
| bmh | Block Partitioning |
| co | Crossover Detection |
| cs | Chromosome Splitter |
| dot-fastdist | Calculate Genotypic Distances |
| dot-fillGap | Fill gaps in a paternal strand vector (native routine... |
| dot-fixBothStrand | Fix conflicting allele assignments on both haplotype strands |
| dot-fixRotation | Fix strand label rotation across consecutive block-structure... |
| dot-hblock | Build haplotype blocks from a BMH result matrix (native... |
| dot-ibdCluster | Cluster individuals by local IBD-like similarity in sliding... |
| dot-maf | Calculate minor allele frequency (MAF) |
| dot-o2tH | Convert a one-row haplotype to a two-row haplotype |
| dot-phfnoGenotype | Phase half-sib paternal haplotype using blocks and sire... |
| dot-prCalus | Calus-style recursive clustering of individuals using an OH... |
| dot-prManual | Manual recursive clustering using an OH matrix and a fixed... |
| dot-prSimple | Simple recursive clustering using an OH matrix with a linear... |
| dot-ptr2por | Convert a two-row haplotype per individual to a one-row... |
| dot-rpohhsphase | Reconstruct half-sib groups by recursive clustering with a... |
| dot-simulateHalfsib | Simulate Half-Sibling Genotypes |
| fixSW | Fixing Switch Errors |
| genotypes | Example Genotype Data Set |
| groupMatSingle | Grouping a Half-sib Family |
| hbp | Haplotype Blocks of Phased Data |
| hh | Heatmap of Half-sibs |
| hsphase-package | Phasing, Pedigree Reconstruction, Sire Imputation and... |
| hss | Half-sib Family Splitter |
| imageplot | Image Plot of Blocking Structure |
| impute | Impute of Low Density SNP Marker to High Density (Paternal... |
| map | Example Map File |
| ohd | Opposing Homozygote Detection |
| ohg | Matrix of Opposing Homozygotes |
| ohplot | Opposing Homozygotes Plot |
| para | Parallel Analysis of Data |
| pedigree | Example Pedigree |
| pedigreeNaming | Fix Pedigree Errors |
| phf | Half-sib Family Phasing |
| pm | Probability Matrix |
| pogc | Parent-Offspring Group Constructor |
| readGenotype | Read and Check the Genotype File |
| recombinations | Recombination Number |
| rplot | Recombination Plot |
| rpoh | Reconstruct Pedigree Based on Matrix of Opposing Homozygotes |
| ssp | Sire Imputation and Phasing |
| switchDetector | Switch Detector |
