Self Organizing Maps (SOM): Example using RNAseq reads

Written by: Ciera Martinez

Tutorial is for learning about how to run clustering analysis using Self Organizing Maps using the kohonen package in R.

part 1: Cleaning EdgeR output for SOM analysis.

part 2a: Running PCA and SOM

part 2b: Running superSOM

part 3b: Further visualization to understand results

Running Code

To run examples, please download all files from Github Repository page and keep files in the same folders they were downloaded in. Open .Rmd files in Rstudio and set working directory to directory in which code was opened in .r. (Session > Set Working Directory > To Source File Location)

New to Github?: There is a green button that says “clone or download”, there is a “download” zip file option here.

Directory Structure of Repository

data: Data need to run tutorials. Including output, input, and required data for further analysis after running SOMs.

pdf: Knitted output PDFs from the .Rmd files.

html: knitted output html from .Rmd files.

r: Rmd R markdown files with all original code. Please set working directory to this directory to run all code.