Rodrigo R. Amadeu

Rodrigo R. Amadeu

Quantitative Genetics

Collection of posts (R and more!)

less than 1 minute read

Published:

Links to R tips and misc stuff

R Codes/Packages

function: Multiple graphs on one page (ggplot2)

cowplot: Multiple Plots with ggplot2

A list of great R tips

Big Data in R Webinar

Faster R: Things to not forget

Strategies to Speedup R Code

Run a Remote R Session: emacs+ess+r+ssh

Mapping in R using ggplot2

R Graph Catalog

R Graph Gallery

How to Shiny! :D

Templates

Article/Report in Rmd

Something about LaTeX

LaTeX symbols collection

LaTeX table generator

Emacs

OrgMode Tutorial

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BGLR with Reps

less than 1 minute read

Published:

To fit a model that has reps or any unbalanced design in BGLR, you need to first design the Z matrix, you can use model.matrix function for that. Then, in the ETA object you need to provide a ZGZ’ or ZM instead of standard X or K matrices. More on it here. Example below:

Common cases that the GRM doesn’t invert

5 minute read

Published:

Here, I show common genetic reasons where can lead to genomic relationship matrix (GRM) with problems in the inversion. They are commonly based on population structure or repeated (or highly similar) information. The cases are not always true, but they can represent why you have a strong linear dependence in your G matrix (Van Raden 2008) and a not unique inverse for the matrix. After identifying the reason, you can take action in order to manage the data before building the G matrix.

R Parallel with Genomic Prediction Application

5 minute read

Published:

Material developed for a workshop on R Parallel with Genomic Selection Application for the Genomic Selection Studies group at University of Florida, Gainesville, FL.

Introduction to R

26 minute read

Published:

For beginners with focus on Bioinformatics and Genetics