| Type: | Package |
| Title: | Tool for Clustering Genotypes in Haplotypes |
| Version: | 0.1 |
| Date: | 2016-03-28 |
| Author: | Sebastian Simondi <sebastian.simondi@gmail.com> and Gaston Quero, with contributions from Victoria Bonnecarrere and Lucia Gutierrez |
| Maintainer: | Gaston Quero <gastonquero@gmail.com> |
| 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. |
| Depends: | R (≥ 2.10) |
| License: | GPL-3 |
| LazyData: | TRUE |
| RoxygenNote: | 5.0.1 |
| Suggests: | knitr, rmarkdown, testthat |
| VignetteBuilder: | knitr |
| Imports: | graphics, utils |
| NeedsCompilation: | no |
| Packaged: | 2016-04-06 14:44:27 UTC; GQ |
| Repository: | CRAN |
| Date/Publication: | 2016-04-06 17:23:47 |
haplotyper function identifies haplotypes within QTL.
Description
This function groups together all individuals of a population with the same haplotype.
Usage
haplotyper(x, Print = FALSE)
Arguments
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 |
Details
Each group contains individual with the same allele in each SNP, whether or not missing data.
Value
a matrix with the haplotypes
Author(s)
Sebastian Simondi, Victoria Bonnecarrere, Lucia Gutierrez, Gaston Quero
See Also
read.table function
Examples
## Not run:
data(rice_qtl)
haplotyper(rice_qtl)
## End(Not run)
Real experimental data
Description
The data is a QTL for rice Grain Quality
Usage
rice_qtl
Format
A data frame 326 rows (individual) and 38 variables (SNPs)
Source
Uruguayan Rice Breeding GWAS (URiB)
simple QTL simulated
Description
A dataset containing the marcadores
Usage
sim_qtl
Format
A data frame 5 rows (individuals) and 7 variables (snps)
Source
simulated data