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hsphase (version 2.0.1)

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

2.0.1

License

GPL (>= 3)

Maintainer

Mohammad Ferdosi

Last Published

December 5th, 2016

Functions in hsphase (2.0.1)

co

Crossover Detection
pogc

Parent Offspring Group Constructor
ohd

Opposing Homozygote Detection
readGenotype

Read and Check the Genotype File
pedigree

Example Pedigree
hh

Heatmap of Half-sibs
rpoh

Reconstruct Pedigree Based on Matrix of Opposing Homozygotes
pedigreeNaming

Fix Pedigree Errors
para

Parallel Analysis of Data
phf

Half-Sib Family Phasing
pm

Probability Matrix
impute

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

Block Partitioning
hsphase-package

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

Haplotype Blocks of Phased Data
map

Example of Map File
ssp

Sire Imputation and Phasing
cs

Chromosome Splitter
ohg

Matrix of Opposing Homozygotes
imageplot

Image Plot of Blocking Structure
rplot

Recombination Plot
hss

Half-sib Family Splitter
genotypes

Example of Genotype Data Set
recombinations

Recombination Number
aio

All-in-one Phasing
ohplot

Opposing Homozygotes Plot