Package: hsphase 3.0.1

Mohammad Ferdosi

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

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

Authors:Mohammad Ferdosi [aut, cre], Cedric Gondro [aut]

# Install 'hsphase' in R:

install.packages('hsphase', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

Last updated from:4019055bdb. Checks:6 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	167
linux-devel-x86_64	OK	201
source / vignettes	OK	254
linux-release-arm64	OK	151
linux-release-x86_64	OK	191
wasm-release	OK	180

Last update: 2026-02-17
Started: 2013-05-25

Help page	Topics
Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events for Half-sib Families	hsphase-package hsphase
Calculate Genotypic Distances	.fastdist
Fix strand label rotation across consecutive block-structure columns	.fixRotation
Build haplotype blocks from a BMH result matrix (native routine wrapper)	.hblock
Calculate minor allele frequency (MAF)	.maf
Convert a one-row haplotype to a two-row haplotype	.o2tH
Convert a two-row haplotype per individual to a one-row representation	.ptr2por
Simulate Half-Sibling Genotypes	.simulateHalfsib
Add Switches	addSwitch
All-in-one Phasing	aio
Block Partitioning	bmh
Crossover Detection	co
Chromosome Splitter	cs
Fixing Switch Errors	fixSW
Example Genotype Data Set	genotypes
Grouping a Half-sib Family	groupMatSingle
Haplotype Blocks of Phased Data	hbp
Heatmap of Half-sibs	hh
Half-sib Family Splitter	hss
Image Plot of Blocking Structure	imageplot
Impute of Low Density SNP Marker to High Density (Paternal Strand)	impute
Example Map File	map
Opposing Homozygote Detection	ohd
Matrix of Opposing Homozygotes	ohg
Opposing Homozygotes Plot	ohplot
Parallel Analysis of Data	para
Example Pedigree	pedigree
Fix Pedigree Errors	pedigreeNaming
Half-sib Family Phasing	phf
Probability Matrix	pm
Parent-Offspring Group Constructor	pogc
Read and Check the Genotype File	readGenotype
Recombination Number	recombinations
Recombination Plot	rplot
Reconstruct Pedigree Based on Matrix of Opposing Homozygotes	rpoh
Sire Imputation and Phasing	ssp
Switch Detector	switchDetector