haplotyper: Tool for Clustering Genotypes in Haplotypes
Version 0.1

Function to identify haplotypes within QTL (Quantitative Trait Loci). One haplotype is a combination of SNP (Single Nucleotide Polymorphisms) within the QTL. This function 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, haplotyper groups individuals, that to be imputed, have a non-zero probability of having the same alleles in the entire sequence of SNP's. Moreover, haplotyper calculates such probability from relative frequencies.

Browse man pages Browse package API and functions Browse package files

AuthorSebastian Simondi <sebastian.simondi@gmail.com> and Gaston Quero, with contributions from Victoria Bonnecarrere and Lucia Gutierrez
Date of publication2016-04-06 17:23:47
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("haplotyper")

Man pages

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

Functions

haplotyper Man page Source code
rice_qtl Man page
sim_qtl Man page

Files

inst
inst/doc
inst/doc/haplotyper_vignette.html
inst/doc/haplotyper_vignette.Rmd
inst/doc/haplotyper_vignette.R
NAMESPACE
data
data/rice_qtl.RData
data/sim_qtl.RData
R
R/sim_qtl.R
R/haplotyper.R
R/rice_qtl.R
vignettes
vignettes/haplotyper_vignette.Rmd
vignettes/haplotyper_reports
vignettes/haplotyper_reports/haplotyper_result.txt
vignettes/haplotyper_reports/haplotypes.txt
vignettes/haplotyper_reports/haplotypes_frequencies.txt
vignettes/haplotyper_reports/undeterminates.txt
vignettes/haplotyper_reports/duplicates.txt
MD5
build
build/vignette.rds
DESCRIPTION
man
man/rice_qtl.Rd
man/haplotyper.Rd
man/sim_qtl.Rd
haplotyper documentation built on May 19, 2017, 5:32 p.m.