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hsphase (version 1.2.5)

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

1.2.5

License

GPL (>= 3)

Maintainer

Mohammad Ferdosi

Last Published

February 21st, 2014

Functions in hsphase (1.2.5)

hh

Heatmap of Half-sibs
ohplot

Opposing Homozygotes Plot
ohg

Matrix of Opposing Homozygotes
genotypes

Example Genotype Data Set
hbp

Haplotype Blocks of Phased Data
hsphase-package

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

Fix Pedigree Errors
rplot

Recombination Plot
rpoh

Reconstruct Pedigree Based on Matrix of Opposing Homozygotes
co

Crossover Detection
imageplot

Image Plot of Blocking Structure
map

Example Map File
ssp

Sire Imputation and Phasing
aio

All-in-one Phasing
hss

Half-sib Family Splitter
readGenotype

Read and Check the Genotype File
para

Parallel Analysis of Data
pedigree

Example Pedigree
pm

Probability Matrix
bmh

Block Partitioning
recombinations

Recombination Number
pogc

Parent Offspring Group Constructor
phf

Half-Sib Family Phasing
ohd

Opposing Homozygote Detection
impute

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

Chromosome Splitter