hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data
Version 2.0.1

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

AuthorMohammad Ferdosi <mferdosi@myune.edu.au>, Cedric Gondro <cgondro2@une.edu.au>
Date of publication2016-12-05 18:28:47
MaintainerMohammad Ferdosi <mferdosi@myune.edu.au>
LicenseGPL (>= 3)
Version2.0.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("hsphase")

Getting started

Package overview

Popular man pages

bmh: Block Partitioning
co: Crossover Detection
hh: Heatmap of Half-sibs
hsphase-package: Phasing, Pedigree Reconstruction, Sire Imputation and...
imageplot: Image Plot of Blocking Structure
ohd: Opposing Homozygote Detection
rplot: Recombination Plot
See all...

All man pages Function index File listing

Man pages

aio: All-in-one Phasing
bmh: Block Partitioning
co: Crossover Detection
cs: Chromosome Splitter
genotypes: Example of Genotype Data Set
hbp: Haplotype Blocks of Phased Data
hh: Heatmap of Half-sibs
hsphase-package: Phasing, Pedigree Reconstruction, Sire Imputation and...
hss: Half-sib Family Splitter
imageplot: Image Plot of Blocking Structure
impute: Impute of Low Density SNP Marker to High Density (Paternal...
map: Example of Map File
ohd: Opposing Homozygote Detection
ohg: Matrix of Opposing Homozygotes
ohplot: Opposing Homozygotes Plot
para: Parallel Analysis of Data
pedigree: Example Pedigree
pedigreeNaming: Fix Pedigree Errors
phf: Half-Sib Family Phasing
pm: Probability Matrix
pogc: Parent Offspring Group Constructor
readGenotype: Read and Check the Genotype File
recombinations: Recombination Number
rplot: Recombination Plot
rpoh: Reconstruct Pedigree Based on Matrix of Opposing Homozygotes
ssp: Sire Imputation and Phasing

Functions

Files

inst
inst/CITATION
inst/doc
inst/doc/hsphase.R
inst/doc/hsphase.pdf
inst/doc/hsphase.Rnw
src
src/co.h
src/Makevars
src/block4Phase.cpp
src/TypeConversion.h
src/MAF.cpp
src/Ohd.cpp
src/oh.h
src/TypeConversion.cpp
src/FastDist.cpp
src/swDetect.cpp
src/memory.h
src/hsp.h
src/co.cpp
src/hsp.cpp
src/swDetect.h
src/diag.h
src/Ohd.h
src/main.cpp
src/MAF.h
src/diag.cpp
src/block.cpp
src/memory.cpp
src/Makevars.win
src/block4Phase.h
src/FastDist.h
src/oh.cpp
src/block.h
NAMESPACE
demo
demo/hsphase.R
demo/00Index
data
data/pedigree.txt.gz
data/genotypes.rda
data/map.txt.gz
R
R/ohg.R
R/prSimple.R
R/hss.R
R/bmh.R
R/impute.R
R/ohd.R
R/co.R
R/rplot.R
R/hh.R
R/fastDist.R
R/pogc.R
R/simulateHalfsib.R
R/hsphase.R
R/prManual.R
R/namingInferedPedigree.R
R/cs.R
R/prCalus.R
R/ohplot.R
R/para.R
R/ssp.R
R/maf.R
R/rpohhsphase.R
R/aio.R
R/rpoh.R
R/imageplot.R
vignettes
vignettes/hsphase.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/pm.Rd
man/aio.Rd
man/cs.Rd
man/phf.Rd
man/bmh.Rd
man/map.Rd
man/pogc.Rd
man/ohd.Rd
man/ohplot.Rd
man/rpoh.Rd
man/readGenotype.Rd
man/recombinations.Rd
man/genotypes.Rd
man/ohg.Rd
man/co.Rd
man/pedigreeNaming.Rd
man/para.Rd
man/pedigree.Rd
man/hh.Rd
man/hbp.Rd
man/imageplot.Rd
man/impute.Rd
man/ssp.Rd
man/hss.Rd
man/rplot.Rd
man/hsphase-package.Rd
hsphase documentation built on May 19, 2017, 3:25 p.m.

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