haplotyper: Tool for Clustering Genotypes in Haplotypes

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.

Author
Sebastian Simondi <sebastian.simondi@gmail.com> and Gaston Quero, with contributions from Victoria Bonnecarrere and Lucia Gutierrez
Date of publication
2016-04-06 17:23:47
Maintainer
Gaston Quero <gastonquero@gmail.com>
License
GPL-3
Version
0.1

View on CRAN

Man pages

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

Files in this package

haplotyper
haplotyper/inst
haplotyper/inst/doc
haplotyper/inst/doc/haplotyper_vignette.html
haplotyper/inst/doc/haplotyper_vignette.Rmd
haplotyper/inst/doc/haplotyper_vignette.R
haplotyper/NAMESPACE
haplotyper/data
haplotyper/data/rice_qtl.RData
haplotyper/data/sim_qtl.RData
haplotyper/R
haplotyper/R/sim_qtl.R
haplotyper/R/haplotyper.R
haplotyper/R/rice_qtl.R
haplotyper/vignettes
haplotyper/vignettes/haplotyper_vignette.Rmd
haplotyper/vignettes/haplotyper_reports
haplotyper/vignettes/haplotyper_reports/haplotyper_result.txt
haplotyper/vignettes/haplotyper_reports/haplotypes.txt
haplotyper/vignettes/haplotyper_reports/haplotypes_frequencies.txt
haplotyper/vignettes/haplotyper_reports/undeterminates.txt
haplotyper/vignettes/haplotyper_reports/duplicates.txt
haplotyper/MD5
haplotyper/build
haplotyper/build/vignette.rds
haplotyper/DESCRIPTION
haplotyper/man
haplotyper/man/rice_qtl.Rd
haplotyper/man/haplotyper.Rd
haplotyper/man/sim_qtl.Rd