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hsphase (version 2.0.4)

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

278

Version

2.0.4

License

GPL-3

Maintainer

Mohammad Ferdosi

Last Published

April 6th, 2025

Functions in hsphase (2.0.4)

pedigree

Example Pedigree Data Set
.maf

Calculate Minor Allele Frequency (MAF)
pm

Probability Matrix
hsphase-package

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

Half-sib Family Splitter
pogc

Parent Offspring Group Constructor
ohplot

Opposing Homozygotes Plot
ssp

Sire Imputation and Phasing
imageplot

Image Plot of Blocking Structure
impute

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

Half-Sib Family Phasing
pedigreeNaming

Fix Pedigree Errors
ohd

Opposing Homozygote Detection
map

Example Map File for Genetic Data
rplot

Recombination Plot
rpoh

Reconstruct Pedigree Based on Matrix of Opposing Homozygotes
.simulateHalfsib

Simulate Half-Sibling Genotypes
hbp

Haplotype Blocks of Phased Data
hh

Heatmap of Half-sibs
co

Crossover Detection
genotypes

Example of Genotype Data Set
bmh

Block Partitioning
aio

All-in-one Phasing
cs

Chromosome Splitter
.fastdist

Calculate Genotypic Distances
para

Parallel Analysis of Data
ohg

Matrix of Opposing Homozygotes
readGenotype

Read and Check the Genotype File
recombinations

Recombination Number