flagme

Version: 1.34.0

Website

https://bioconductor.org/packages/release/bioc/html/flagme.html

Description

This bioconductor package processes and visualises GC-MS samples. It does not include support for peak detection (this can be done using AMDIS or ChromaTOF). It uses a dynamic programming-based alignment strategy - a similarity matrix is calculated based on a scoring function, taking into account similarity in RT and of the apex spectra, meaning that there are two components to the similarity: spectra and RT. A gap parameter must be set, with a high gap penalty discouraging gaps of peaks between spectra and a low gap penalty having very little cost for gaps (it is recommended to use 0.4-0.6). Similarly "D" modulates the penalty for RT difference penalty. Provides visualisation of total ion current (TIC) or extracted ion current (XIC) and 2D heat maps of intensity for individual samples.

Functionality

• Preprocessing

Instrument Data Type

• MS/GC-MS

Approaches

Computer Skills

Advanced

Software Type

R Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

gcspikelite, xcms, CAMERA

Input Formats - Open

AMDIS.elu

Input Formats - Proprietary

ChromaTOF

Published

2014

Last Updated

2017

License

LGPL (>=2)

Paper

PMID