clusterhap: Clustering Genotypes in Haplotypes

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.

Install the latest version of this package by entering the following in R:
install.packages("clusterhap")
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

View on CRAN

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

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