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hsphase (version 1.2.6)

Phasing and imputation 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

1.2.6

License

GPL (>= 3)

Maintainer

Mohammad Ferdosi

Last Published

April 2nd, 2014

Functions in hsphase (1.2.6)

hsphase-package

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

Read and Check the Genotype File
hss

Half-sib Family Splitter
recombinations

Recombination Number
ohplot

Opposing Homozygotes Plot
ohd

Opposing Homozygote Detection
bmh

Block Partitioning
hh

Heatmap of Half-sibs
ssp

Sire Imputation and Phasing
ohg

Matrix of Opposing Homozygotes
map

Example of Map File
genotypes

Example of Genotype Data Set
rplot

Recombination Plot
imageplot

Image Plot of Blocking Structure
aio

All-in-one Phasing
pedigreeNaming

Fix Pedigree Errors
cs

Chromosome Splitter
hbp

Haplotype Blocks of Phased Data
rpoh

Reconstruct Pedigree Based on Matrix of Opposing Homozygotes
phf

Half-Sib Family Phasing
pedigree

Example Pedigree
co

Crossover Detection
pm

Probability Matrix
impute

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

Parallel Analysis of Data
pogc

Parent Offspring Group Constructor