AutoEmma

Automated Efficient Mixed Model Association Studies - R Package

Installation

1. Download AutoEmma_1.2.2.tar.gz from GitHub.
2. Open R-Studio and type the following command into the Console.

   install.packages("file/path/AutoEmma_1.2.2.tar.gz", repos = NULL, type = "Source")

Quick Tutorial

1. Load AutoEmma Package into your current R session: library(AutoEmma)
2. Create diagnostic graphs for your input files: ae.input.graphs(gfile = "your_genotypes.csv", pfile = "your_phenotypes.csv")
3. Create a map file: my_map <- ae.make.map(file = "your_phenotypes.csv")
4. Run AutoEmma: results <- ae.run(genotype = "your_genotypes.csv", phenotype = "your_phenotypes.csv", map = my_map, method = "REML")
5. Customize graphs if desired: ae.manhattan(df = results, file_name = "new_manhattan.png", point_size = 1.2, colors = c("royalblue3", "gray18"), title = "Manhattan Plot", sl = 4.5, pval = 0.05, snps = 100000, exclude = 0.5, annotate = TRUE)

Change Log

Version 1.0.0

• Initial release

Version 1.0.1

• Simplified input diagnostic graphs
• Fixed a bug in strain selection for cladogram creation

Version 1.1.1

• Improved manhattan and Q-Q plots
• Added annotation of suggestive SNPs to manhattan plot

Version 1.2.0

• Added SEM option to average phenotype plot
• Improved look of input diagnostics graphs
• Vectorized averages calculation to speed up input diagnostics graphs

Version 1.2.1

• Added option to choose between wide-screen graphs (16x9) and square graphs (9x9)
• Improved text updates for input diagnostic graphs

Version 1.2.2

• Removed reference in documentation to non-existent kinship use option
• Added support for generating kinship matrix using all snps or only snps where all strains have information.