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hsphase (version 1.2.4)

Phasing and imputation of half-sib families using SNP data

Description

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

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Version

Install

install.packages('hsphase')

Monthly Downloads

273

Version

1.2.4

License

GPL (>= 3)

Maintainer

Mohammad Ferdosi

Last Published

October 30th, 2013

Functions in hsphase (1.2.4)

co

Crossover Detection
map

Example Map File
cs

Chromosome Splitter
phf

Half-Sib Family Phasing
pedigreeNaming

Fix Pedigree Errors
bmh

Block Partitioning
ohg

Matrix of Opposing Homozygotes
hh

Heatmap of Half-sibs
readGenotype

Read and Check the Genotype File
impute

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

Opposing Homozygote Detection
hbp

Haplotype Blocks of Phased Data
ssp

Sire Imputation and Phasing
imageplot

Image Plot of Blocking Structure
rplot

Recombination Plot
pedigree

Example Pedigree
para

Parallel Analysis of Data
recombinations

Recombination Number
aio

All-in-one Phasing
pm

Probability Matrix
genotypes

Example Genotype Data Set
hss

Half-sib Family Splitter
hsphase-package

Phasing, Sire Imputation and Recombination Events for Half-sib Families
rpoh

Reconstruct Pedigree Based on Matrix of Opposing Homozygotes