clusterhap: Clustering Genotypes in Haplotypes

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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.

Author
Gaston Quero <gastonquero@gmail.com> and Sebastian Simondi <sebastian.simondi@gmail.com> , with contributions from Victoria Bonnecarrere and Lucia Gutierrez
Date of publication
2016-05-16 14:37:36
Maintainer
Gaston Quero <gastonquero@gmail.com>
License
GPL-3
Version
0.1

View on CRAN

Man pages

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

Files in this package

clusterhap
clusterhap/inst
clusterhap/inst/doc
clusterhap/inst/doc/clusterhap_vignette.Rmd
clusterhap/inst/doc/clusterhap_vignette.R
clusterhap/inst/doc/clusterhap_vignette.html
clusterhap/NAMESPACE
clusterhap/data
clusterhap/data/rice_qtl.RData
clusterhap/data/sim_qtl.RData
clusterhap/R
clusterhap/R/sim_qtl.R
clusterhap/R/rice_qtl.R
clusterhap/R/clusterhap.R
clusterhap/vignettes
clusterhap/vignettes/clusterhap_vignette.Rmd
clusterhap/vignettes/clusterhap_reports
clusterhap/vignettes/clusterhap_reports/haplotypes.txt
clusterhap/vignettes/clusterhap_reports/haplotypes_result.txt
clusterhap/vignettes/clusterhap_reports/haplotypes_frequencies.txt
clusterhap/vignettes/clusterhap_reports/undeterminates.txt
clusterhap/vignettes/clusterhap_reports/duplicates.txt
clusterhap/MD5
clusterhap/build
clusterhap/build/vignette.rds
clusterhap/DESCRIPTION
clusterhap/man
clusterhap/man/clusterhap.Rd
clusterhap/man/rice_qtl.Rd
clusterhap/man/sim_qtl.Rd