cosmiq

Version: 1.12.0

Website

http://bioconductor.org/packages/release/bioc/html/cosmiq.html

Description

This bioconductor package provides preprocessing for LC-MS or GC-MS metabolomics or lipidomics data. It is designed to improve the detection of low abundance signals by generating a master map of all mz/RT space before the peak detection algorithm is applied. It is built using the xcmsSet object structure and so can be integrated with xcms (it is suggested to use retcor.orbiwarp for RT alignment). It uses a continuous wavelet transformation (CWT) peak detection algorithm adapted from Du et al 2006. It includes the "quality_combined" function which is designed for use when there is no RT information available, so is suitable for peak picking of direct infusion experiments.

Functionality

• Preprocessing

Instrument Data Type

• MS/GC-MS
• MS/LC-MS

Approaches

• Untargeted

Computer Skills

Advanced

Software Type

R Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

R (≥ 3.0.2), Rcpp

Input Formats - Open

mzData, mzML, mzXML, netCDF

Input Formats - Proprietary

N/A

Published

2014

Last Updated

2017

License

GPL-3

Paper

PMID