Introduction to the Alpha Version
R code has been written to streamline the analysis of typical plant breeding experiments in which sets of genotypes have been evaluated in one or more environments (locations, years, seasons). To further ease the analysis, a graphical user interface (GUI) has been created around it, releasing the user from the need to write the necessary R code. This code is meant to be the first component of a more comprehensive analytical pipeline, in which the outputs from these analyses are used for QTL detection using conventional QTL mapping and association mapping methods.
The code allows for two major types of analyses: a) single trial analysis using raw data (plot data), and b) multi-environment analysis or GxE analysis using a genotype by environment table of means. Typically, one will first perform an analysis per trial to compile tables of adjusted means, and use the compiled genotype by environment tables of means in a subsequent GxE analysis.