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hsphase (version 3.0.0)

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

Description

Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data.

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Version

Install

install.packages('hsphase')

Monthly Downloads

273

Version

3.0.0

License

GPL-3

Maintainer

Mohammad Ferdosi

Last Published

February 17th, 2026

Functions in hsphase (3.0.0)

Calus-style recursive clustering of individuals using an OH matrix

Calculate minor allele frequency (MAF)

Convert a two-row haplotype per individual to a one-row representation

Convert a one-row haplotype to a two-row haplotype

Reconstruct half-sib groups by recursive clustering with a recombination stop rule

Phase half-sib paternal haplotype using blocks and sire haplotypes (no offspring genotype needed)

Manual recursive clustering using an OH matrix and a fixed threshold

Simple recursive clustering using an OH matrix with a linear threshold rule

Cluster individuals by local IBD-like similarity in sliding windows

.simulateHalfsib

Simulate Half-Sibling Genotypes

hsphase-package

Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events for Half-sib Families

Half-sib Family Splitter

Image Plot of Blocking Structure

Example Map File

Impute of Low Density SNP Marker to High Density (Paternal Strand)

Heatmap of Half-sibs

Probability Matrix

Example Genotype Data Set

Fixing Switch Errors

Half-sib Family Phasing

Opposing Homozygotes Plot

Parent-Offspring Group Constructor

Opposing Homozygote Detection

Recombination Number

Matrix of Opposing Homozygotes

Parallel Analysis of Data

Recombination Plot

Reconstruct Pedigree Based on Matrix of Opposing Homozygotes

Sire Imputation and Phasing

Switch Detector

Example Pedigree

Fix Pedigree Errors

Read and Check the Genotype File

Haplotype Blocks of Phased Data

Grouping a Half-sib Family

Chromosome Splitter

Calculate Genotypic Distances

Build haplotype blocks from a BMH result matrix (native routine wrapper)

Fix strand label rotation across consecutive block-structure columns

Fill gaps in a paternal strand vector (native routine wrapper)

Crossover Detection

Fix conflicting allele assignments on both haplotype strands

All-in-one Phasing

Block Partitioning