MSeasy: Preprocessing of Gas Chromatography-Mass Spectrometry (GC-MS) data
Version 5.3.3

Package for the detection of molecules in complex mixtures of compounds. It creates an initial_DATA matrix from several GC-MS analyses by collecting and assembling the information from chromatograms and mass spectra (MS.DataCreation), It can read several format (ASCII, CDF, mzML, mzXML or mzData).It tests for the best unsupervised clustering method to group similar mass spectra into molecules (MS.test.clust).It runs the optimal unsupervised clustering method on the initial_DATA matrix, identifies the optimal number of clusters, produces different files for facilitating the quality control and identification of putative molecules, and returns fingerprinting or profiling matrices (MS.clust).It converts output files from MS.clust for NIST mass spectral library search and ARISTO webtool search

AuthorElodie Courtois <courtoiselodie@gmail.com>, Yann Guitton <yann.guitton@gmail.com>, Florence Nicole <florence.nicole@univ-st-etienne.fr>
Date of publication2013-03-20 17:07:31
MaintainerYann GUITTON <yann.guitton@gmail.com>
LicenseGPL-2
Version5.3.3
URL http://sites.google.com/site/rpackagemseasy/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MSeasy")

Getting started

Package overview

Popular man pages

Agilent_quantF_MSclust: Demonstration dataset for MS.clust
ASCII_TransASCII: Demonstration folder for trans.ASCII
Data_testclust: Demonstration dataset for MS.test.clust
MS.clust: Mass spectra clustering and creation of a fingerprinting or...
MS.DataCreation: an initial data from GC-MS analyses by collecting and...
MSeasyToMSP: Convert output files from MS.clust into MSP format for NIST...
MS.test.clust: Test for the best clustering method
See all...

All man pages Function index File listing

Man pages

Agilent_MSDataCreation: Demonstration folder for MS.DataCreation with option...
Agilent_quantF_MSclust: Demonstration dataset for MS.clust
Agilent_quantT_MSclust: Demonstration dataset for MS.clust
ASCII_MSclust: Demonstration dataset for MS.clust
ASCII_MSDataCreation: Demonstration folder for MS.DataCreation with option...
ASCII_TransASCII: Demonstration folder for trans.ASCII
Data_testclust: Demonstration dataset for MS.test.clust
MS.clust: Mass spectra clustering and creation of a fingerprinting or...
MS.DataCreation: an initial data from GC-MS analyses by collecting and...
MSeasy-package: Unsupervised and untargeted processing of Gas...
MSeasyToARISTO: Convert output files from the function MS.clust into...
MSeasyToMSP: Convert output files from MS.clust into MSP format for NIST...
MS.test.clust: Test for the best clustering method
SearchNIST: Identification of putative molecules using the NIST mass...
trans.ASCII: Transform GC-MS data in ASCII format to suitable data for...

Functions

ASCII_MSDataCreation Man page
ASCII_MSclust Man page
ASCII_TransASCII Man page
Agilent_MSDataCreation Man page
Agilent_quantF_MSclust Man page
Agilent_quantT_MSclust Man page
Data_testclust Man page
MS.DataCreation Man page Source code
MS.clust Man page Source code
MS.test.clust Man page Source code
MSeasy Man page
MSeasy-package Man page
MSeasyToARISTO Man page Source code
MSeasyToMSP Man page Source code
SearchNIST Man page Source code
trans.ASCII Man page Source code

Files

MD5
R
R/trans.ASCII.R
R/SearchNIST.R
R/MSeasyToMSP.R
R/MSeasyToARISTO.R
R/MS.test.clust.R
R/MS.DataCreation.R
R/MS.clust.R
NAMESPACE
man
man/trans.ASCII.Rd
man/SearchNIST.Rd
man/MSeasyToMSP.Rd
man/MSeasyToARISTO.Rd
man/MSeasy-package.Rd
man/MS.test.clust.Rd
man/MS.DataCreation.Rd
man/MS.clust.Rd
man/Data_testclust.Rd
man/ASCII_TransASCII.Rd
man/ASCII_MSDataCreation.Rd
man/ASCII_MSclust.Rd
man/Agilent_quantT_MSclust.Rd
man/Agilent_quantF_MSclust.Rd
man/Agilent_MSDataCreation.Rd
inst
inst/doc
inst/doc/Output_examples
inst/doc/Output_examples/output_peak21.txt
inst/doc/Output_examples/output_cluster21.txt
inst/doc/Output_examples/ForNIST.msp
inst/doc/MSeasy-manual.pdf
inst/doc/ASCII_TransASCII
inst/doc/ASCII_TransASCII/ASCII_2.txt
inst/doc/ASCII_TransASCII/ASCII_1.txt
inst/doc/ASCII_MSDataCreation
inst/doc/ASCII_MSDataCreation/ASCII_2.txt
inst/doc/ASCII_MSDataCreation/ASCII_1.txt
inst/doc/Agilent_MSDataCreation
inst/doc/Agilent_MSDataCreation/Agilent2.D
inst/doc/Agilent_MSDataCreation/Agilent2.D/rteres.txt
inst/doc/Agilent_MSDataCreation/Agilent1.D
inst/doc/Agilent_MSDataCreation/Agilent1.D/rteres.txt
inst/CITATION
DESCRIPTION
data
data/Data_testclust.rda
data/ASCII_MSclust.rda
data/Agilent_quantT_MSclust.rda
data/Agilent_quantF_MSclust.rda
ChangeLog
MSeasy documentation built on May 19, 2017, 11:34 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

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