clusterhap: Clustering Genotypes in Haplotypes
Version 0.1

One haplotype is a combination of SNP (Single Nucleotide Polymorphisms) within the QTL (Quantitative Trait Loci). clusterhap groups together all individuals of a population with the same haplotype. Each group contains individual with the same allele in each SNP, whether or not missing data. Thus, clusterhap groups individuals, that to be imputed, have a non-zero probability of having the same alleles in the entire sequence of SNP's. Moreover, clusterhap calculates such probability from relative frequencies.

AuthorGaston Quero <gastonquero@gmail.com> and Sebastian Simondi <sebastian.simondi@gmail.com> , with contributions from Victoria Bonnecarrere and Lucia Gutierrez
Date of publication2016-05-16 14:37:36
MaintainerGaston Quero <gastonquero@gmail.com>
LicenseGPL-3
Version0.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("clusterhap")

Getting started

Use clusterhap"

Popular man pages

clusterhap: clusterhap function identifies haplotypes within QTL.
rice_qtl: Real experimental data
sim_qtl: simple QTL simulated
See all...

All man pages Function index File listing

Man pages

clusterhap: clusterhap function identifies haplotypes within QTL.
rice_qtl: Real experimental data
sim_qtl: simple QTL simulated

Functions

clusterhap Man page Source code
rice_qtl Man page
sim_qtl Man page

Files

inst
inst/doc
inst/doc/clusterhap_vignette.Rmd
inst/doc/clusterhap_vignette.R
inst/doc/clusterhap_vignette.html
NAMESPACE
data
data/rice_qtl.RData
data/sim_qtl.RData
R
R/sim_qtl.R
R/rice_qtl.R
R/clusterhap.R
vignettes
vignettes/clusterhap_vignette.Rmd
vignettes/clusterhap_reports
vignettes/clusterhap_reports/haplotypes.txt
vignettes/clusterhap_reports/haplotypes_result.txt
vignettes/clusterhap_reports/haplotypes_frequencies.txt
vignettes/clusterhap_reports/undeterminates.txt
vignettes/clusterhap_reports/duplicates.txt
MD5
build
build/vignette.rds
DESCRIPTION
man
man/clusterhap.Rd
man/rice_qtl.Rd
man/sim_qtl.Rd
clusterhap documentation built on May 19, 2017, 11:23 a.m.

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