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
In github it is available the experimental version 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.