emmanuelparadis / rmds

RDMS

Reduced Multidimensional Scaling

The reduced multidimensional scaling (RMDS) is a method to analyse very large data sets that could be not be handled by standard multidimensional scaling (MDS). The method is described in a paper in revision.

This repository contains the following files:

• common_files.R with two functions used in the other scripts;
• RMDS_Euclidean.R with code to run the MDS with Euclidean distances (typically continuous data);
• RMDS_DNA.R with functions to run the MDS with DNA sequence data;
• rmds.c C code to be used with the above scripts;
• code.R general-purpose functions as described in the paper;
• application_DNA_HIV_gag.R a script with an application using ~10k sequences from HIV.