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hsphase (version 2.0.3)

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

2.0.3

License

GPL-3

Maintainer

Mohammad Ferdosi

Last Published

February 16th, 2024

Functions in hsphase (2.0.3)

ohg

Matrix of Opposing Homozygotes

.maf

Calculate Minor Allele Frequency (MAF)

.fastdist

Calculate Genotypic Distances

aio

All-in-one Phasing

hsphase-package

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

hss

Half-sib Family Splitter

Chromosome Splitter

para

Parallel Analysis of Data

map

Example Map File for Genetic Data

rplot

Recombination Plot

rpoh

Reconstruct Pedigree Based on Matrix of Opposing Homozygotes

pedigreeNaming

Fix Pedigree Errors

impute

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

imageplot

Image Plot of Blocking Structure

phf

Half-Sib Family Phasing

ohd

Opposing Homozygote Detection

pedigree

Example Pedigree Data Set

ssp

Sire Imputation and Phasing

ohplot

Opposing Homozygotes Plot

Probability Matrix

pogc

Parent Offspring Group Constructor

recombinations

Recombination Number

readGenotype

Read and Check the Genotype File

Crossover Detection

.simulateHalfsib

Simulate Half-Sibling Genotypes

genotypes

Example of Genotype Data Set

hbp

Haplotype Blocks of Phased Data

Heatmap of Half-sibs

bmh

Block Partitioning