# Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

## Documentation for package ‘hsphase’ version 3.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.

## Help Pages

hsphase-package | Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events for Half-sib Families
.fastdist | Calculate Genotypic Distances
.fixRotation | Fix strand label rotation across consecutive block-structure columns
.hblock | Build haplotype blocks from a BMH result matrix (native routine wrapper)
.maf | Calculate minor allele frequency (MAF)
.o2tH | Convert a one-row haplotype to a two-row haplotype
.ptr2por | Convert a two-row haplotype per individual to a one-row representation
.simulateHalfsib | Simulate Half-Sibling Genotypes
addSwitch | Add Switches
aio | All-in-one Phasing
bmh | Block Partitioning
co | Crossover Detection
cs | Chromosome Splitter
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 | Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events for Half-sib Families
hss | Half-sib Family Splitter
imageplot | Image Plot of Blocking Structure
impute | Impute of Low Density SNP Marker to High Density (Paternal Strand)
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