CSM Matlab Docs

Getting Started

Welcome to the IMPaCTS toolbox. This is a general purpose Matlab toolbox that covers data import, export, preprocessing and basic analysis of NMR and peak-picked MS spectra.

The features outlined in this documentation represent a standardised interface layer to a large suite of tools for metabolomic analysis developed by internally by researchers in the Division of Computational Systems Medicine at Imperial College London.

This API utilises standardised objects for storing data (csm_spectra) and running analyses (csm_wrapper).

The underlying tools can be accessed via legacy methods, however this not advised as they may unstable.

Requirements

Matlab 2016a
Statistics Toolbox

Installation

Clone or download the repo found on github.
Open Matlab and open pathtool:
```
pathtool
```
Once pathtool opens, click 'Add with subfolders', browse to the location you downloaded the toolbox.
Click the folder, press 'Select Folder'. Matlab will add the folders to the MATLAB search path. Click 'Save' and then 'Close'.
Run the following command and follow the on screen instructions:
```
csm_setup()
```
- When it says 'Please select the IMPaCTS folder’, select the folder in the download folder.
- When it says 'Please select your workspace folder’, select your matlab workspace folder.

That's it. The IMPaCTS Toolbox is now added to the Matlab search path.

Test it by typing help csm_pca into the command window. If it has worked you will see the csm_pca help information.

help csm_pca

NB: You can install the toolbox wherever you want, but make sure you specify the path when prompted.

Using this documentation website

Each Matlab function has a dedicated help section. The help section outlines the description, arguments, returned variables and class methods of the tools.

Either use the menu on the left hand side or use

help csm_tool_name

to see how to use the functions.

Start off with the toolbox data types and the migrations pages to familiarise yourself with the syntax and API objects.