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

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Documentation for package ‘hsphase’ version 2.0.3

• 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