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 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