《R_tools_for_single_and_multiple_trial_analyses_IBP_RPipeline_v0.9》.pdf

IBP_RPipeline v 0.9 R tools for single and multiple trial analyses Sabine Schnabel Gerrit Gort Paul Eilers Willem Kruijer Lucía Gutierrez Marcos Malosetti Fred van Eeuwijk 8th April 2011 Contents 1. Introduction 2 2. Data preparation2 2.1. Project directory 2 2.2. Input files 3 2.2.1 Plot data 3 2.2.2 Genotype by environment means 4 3. Single trial analysis 4 3.1. Running the analysis 5 3.2. Results and output files 7 4. Multiple trial analysis (GxE) 8 4.1. Running the analysis 8 4.2. Results and output files 9 5. Notes about installation. 11 1 | P a g e 1. Introduction 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 interphase (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. In order to perform the analyses, a few conventions should be followed in terms of directory structures and data file formatting.