| Title: | Tool for Clustering Genotypes in Haplotypes |
|---|---|
| Description: | 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. |
| Authors: | Sebastian Simondi <[email protected]> and Gaston Quero, with contributions from Victoria Bonnecarrere and Lucia Gutierrez |
| Maintainer: | Gaston Quero <[email protected]> |
| License: | GPL-3 |
| Version: | 0.1 |
| Built: | 2025-02-13 05:28:49 UTC |
| Source: | https://github.com/cran/haplotyper |
This function groups together all individuals of a population with the same haplotype.
haplotyper(x, Print = FALSE)haplotyper(x, Print = FALSE)
x |
a data.frame that should be loaded with read.table function. Each row represents the individuals while each column represents the markers. The first column contains the names of the genotypes. |
Print |
option for print the haplotyper result. The default is FALSE |
Each group contains individual with the same allele in each SNP, whether or not missing data.
a matrix with the haplotypes
Sebastian Simondi, Victoria Bonnecarrere, Lucia Gutierrez, Gaston Quero
read.table function
## Not run: data(rice_qtl) haplotyper(rice_qtl) ## End(Not run)## Not run: data(rice_qtl) haplotyper(rice_qtl) ## End(Not run)
The data is a QTL for rice Grain Quality
rice_qtlrice_qtl
A data frame 326 rows (individual) and 38 variables (SNPs)
Uruguayan Rice Breeding GWAS (URiB)
A dataset containing the marcadores
sim_qtlsim_qtl
A data frame 5 rows (individuals) and 7 variables (snps)
simulated data