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

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

Author
Mohammad Ferdosi <mferdosi@myune.edu.au>, Cedric Gondro <cgondro2@une.edu.au>
Date of publication
2016-12-05 18:28:47
Maintainer
Mohammad Ferdosi <mferdosi@myune.edu.au>
License
GPL (>= 3)
Version
2.0.1

View on CRAN

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

Files in this package

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