RAMClustR

Version: 0.4

Website

https://github.com/cbroeckl/RAMClustR

Description

This is designed for the analysis of indiscriminate (data-independent-acquisition) MS/MS data that provides a feature grouping method. It takes a dataset preprocessed with XCMS as input (it can take data preprocessed by other software as input, but the user then needs to manually input parameters that are calculated automatically from the xcmsSet). Firstly quantile normalisation is available. If MS/MS data is present, to separate the MS and MS/MS the user can either tag the filename or file path. A custom similarity matrix using two Gaussian terms (one of the different between rt of two features and the other the correlation between two features across all samples) is used to group features. Pearson's correlation is used to calculate similarity. Features that are similar in both Gaussian terms are clustered using a similarity matrix.

Functionality

• Preprocessing

Instrument Data Type

• MS/LC-MS/LC-MS/MS

Approaches

Computer Skills

Advanced

Software Type

R Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

devtools

Input Formats - Open

mzData, mzML, mzXML, netCDF

Input Formats - Proprietary

N/A

Published

2013

Last Updated

2018

License

GPL-2

Paper

http://www.ncbi.nlm.nih.gov/pubmed/24927477

PMID

24927477