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snpReady

A tool to assist breeders to prepare genotypic datasets for genomic analysis in order to run genomic analysis and estimates some population genetics parameters. Thus, it produce outputs that can be use in many packages or softwares related to genomic analysis.

snpReady is available on CRAN

install.packages("snpReady")

The snpReady package has impute package as dependency. However, the package is available at bioconductor. To install this package in the current R version

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("impute")

For older R versions, you need to install the proper Bioconductor version associated, available here

BiocManager::install(version="X.X")

where X.X is the bioconductor version.

The experimental version is available at the github and its installation needs to be done via devtools. Hence, it is necessary first install devtools and later install snpReady

install.packages("devtools")
library(devtools)
install_github("italo-granato/snpReady")

Below, we present some basic usage for the three functions available in snpReady

Function to clean and recode raw dataset from genotyping

data(maize.line)
M <- raw.data(as.matrix(maize.line), frame="long", base=TRUE, sweep.sample= 0.8, 
call.rate=0.95, maf=0.05, input=TRUE, outfile="-101")

Function to create genomic relationship matrix (GRM)

data(maize.hyb)
x <- G.matrix(maize.hyb, method = "VanRaden", format = "wide")
A <- x$Ga
D <- x$Gd

Function to estimate some parameters of genetic of population using markers

data(maize.hyb)
x <- popgen(maize.hyb) 

I would like to thank people from Allogamous Plant Breeding Laboratory Team for helping in this project.

Allogamous Plant Breeding Laboratory Team

To anyone who wants to contribute, please contact Italo Granato for more details.