R package for Genomic Selection with Genotyping-by-Sequencing
This package provides three functions:
GBSPipeline, A function for running the de novo genotyping-by-sequencing pipeline described by Poland et al. (2012). A copy of Tassel 4.0 and Java 1.7 is required to use this function. Tassel 4.0 can be obtained here: http://tassel.bitbucket.org/TasselArchived.html
hap2marker, A function for converting .hap files generated by GBSPipeline into a numeric matrix suitable for the GS.model function.
GS.model, A wrapper function for calculating genomic selection predictions using methods found in other R packages.
This package can be installed in R using the 'devtools' package. Simply load the 'devtools' package and enter the following in R: install_github("gaynorr/GSwGBS")