GHap: Genome-Wide Haplotyping

Haplotype calling from phased SNP data.

Author
Yuri Tani Utsunomiya, Marco Milanesi
Date of publication
2016-06-10 23:28:42
Maintainer
Yuri Tani Utsunomiya <ytutsunomiya@gmail.com>
License
GPL (>= 2)
Version
1.2.1

View on CRAN

Man pages

ancestral
Inference of haplotype origin
assoc
Association analysis for HapAlleles and HapBlocks
blmm
Bayesian linear mixed model
blockgen
Haplotype block generator
blockstats
Block statistics
blup
Convert breeding values into BLUP solutions of HapAllele...
fst
Haplotype Fst
hap2tped
Convert haplotype allele counts to PLINK tped
haplotyping
Haplotype genotypes
hapstats
Haplotype statistics
kinship
Kinship matrix from haplotypes
lmm
Frequentist linear mixed model
loadhaplo
Load haplotype genotype data
loadphase
Load phased genotype data
maf
Compute marker minor allele frequencies
makefile
Create example input files
mergehaplo
Merging GHap.haplo objects
mergephase
Merging GHap.phase objects
mme
Mixed linear model solver
outhaplo
Output GHap.haplo object to a file
outphase
Output GHap.phase object to a file
pca
Principal Components Analysis
profile
Haplotype allele profile
simpheno
Quantitative trait simulation using real HapGenotype data
subsethaplo
Subset GHap.hapo object
subsetphase
Subset GHap.phase object

Files in this package

GHap
GHap/inst
GHap/inst/updates.txt
GHap/inst/extdata
GHap/inst/extdata/HapMap3_chr2.tar.bz2
GHap/inst/doc
GHap/inst/doc/GHap_vignette.pdf
GHap/inst/doc/GHap_vignette.pdf.asis
GHap/NAMESPACE
GHap/R
GHap/R/simpheno.R
GHap/R/ancestral.R
GHap/R/onload.R
GHap/R/pca.R
GHap/R/assoc.R
GHap/R/subsethaplo.R
GHap/R/blockgen.R
GHap/R/hap2tped.R
GHap/R/mergephase.R
GHap/R/haplotyping.R
GHap/R/outhaplo.R
GHap/R/makefile.R
GHap/R/profile.R
GHap/R/loadphase.R
GHap/R/hapstats.R
GHap/R/outphase.R
GHap/R/loadhaplo.R
GHap/R/mme.R
GHap/R/blmm.R
GHap/R/blockstats.R
GHap/R/blup.R
GHap/R/lmm.R
GHap/R/fst.R
GHap/R/mergehaplo.R
GHap/R/subsetphase.R
GHap/R/maf.R
GHap/R/kinship.R
GHap/vignettes
GHap/vignettes/GHap_vignette.pdf.asis
GHap/vignettes/GHap_vignette.Rmd
GHap/MD5
GHap/build
GHap/build/vignette.rds
GHap/DESCRIPTION
GHap/man
GHap/man/loadhaplo.Rd
GHap/man/blockstats.Rd
GHap/man/fst.Rd
GHap/man/loadphase.Rd
GHap/man/blmm.Rd
GHap/man/mme.Rd
GHap/man/subsetphase.Rd
GHap/man/ancestral.Rd
GHap/man/hapstats.Rd
GHap/man/haplotyping.Rd
GHap/man/maf.Rd
GHap/man/hap2tped.Rd
GHap/man/blup.Rd
GHap/man/outhaplo.Rd
GHap/man/outphase.Rd
GHap/man/kinship.Rd
GHap/man/lmm.Rd
GHap/man/simpheno.Rd
GHap/man/pca.Rd
GHap/man/subsethaplo.Rd
GHap/man/mergephase.Rd
GHap/man/makefile.Rd
GHap/man/blockgen.Rd
GHap/man/profile.Rd
GHap/man/assoc.Rd
GHap/man/mergehaplo.Rd