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

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

## Documentation for package ‘hsphase’ version 2.0.4

- 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 Identification for Half-sib Families
.fastdist | Calculate Genotypic Distances
.maf | Calculate Minor Allele Frequency (MAF)
.simulateHalfsib | Simulate Half-Sibling Genotypes
aio | All-in-one Phasing
bmh | Block Partitioning
co | Crossover Detection
cs | Chromosome Splitter
genotypes | Example of Genotype Data Set
hbp | Haplotype Blocks of Phased Data
hh | Heatmap of Half-sibs
hsphase | Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification 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 for Genetic Data
ohd | Opposing Homozygote Detection
ohg | Matrix of Opposing Homozygotes
ohplot | Opposing Homozygotes Plot
para | Parallel Analysis of Data
pedigree | Example Pedigree Data Set
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