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

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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

Author
Elodie Courtois <courtoiselodie@gmail.com>, Yann Guitton <yann.guitton@gmail.com>, Florence Nicole <florence.nicole@univ-st-etienne.fr>
Date of publication
2013-03-20 17:07:31
Maintainer
Yann GUITTON <yann.guitton@gmail.com>
License
GPL-2
Version
5.3.3
URLs

View on CRAN

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...

Files in this package

MSeasy
MSeasy/MD5
MSeasy/R
MSeasy/R/trans.ASCII.R
MSeasy/R/SearchNIST.R
MSeasy/R/MSeasyToMSP.R
MSeasy/R/MSeasyToARISTO.R
MSeasy/R/MS.test.clust.R
MSeasy/R/MS.DataCreation.R
MSeasy/R/MS.clust.R
MSeasy/NAMESPACE
MSeasy/man
MSeasy/man/trans.ASCII.Rd
MSeasy/man/SearchNIST.Rd
MSeasy/man/MSeasyToMSP.Rd
MSeasy/man/MSeasyToARISTO.Rd
MSeasy/man/MSeasy-package.Rd
MSeasy/man/MS.test.clust.Rd
MSeasy/man/MS.DataCreation.Rd
MSeasy/man/MS.clust.Rd
MSeasy/man/Data_testclust.Rd
MSeasy/man/ASCII_TransASCII.Rd
MSeasy/man/ASCII_MSDataCreation.Rd
MSeasy/man/ASCII_MSclust.Rd
MSeasy/man/Agilent_quantT_MSclust.Rd
MSeasy/man/Agilent_quantF_MSclust.Rd
MSeasy/man/Agilent_MSDataCreation.Rd
MSeasy/inst
MSeasy/inst/doc
MSeasy/inst/doc/Output_examples
MSeasy/inst/doc/Output_examples/output_peak21.txt
MSeasy/inst/doc/Output_examples/output_cluster21.txt
MSeasy/inst/doc/Output_examples/ForNIST.msp
MSeasy/inst/doc/MSeasy-manual.pdf
MSeasy/inst/doc/ASCII_TransASCII
MSeasy/inst/doc/ASCII_TransASCII/ASCII_2.txt
MSeasy/inst/doc/ASCII_TransASCII/ASCII_1.txt
MSeasy/inst/doc/ASCII_MSDataCreation
MSeasy/inst/doc/ASCII_MSDataCreation/ASCII_2.txt
MSeasy/inst/doc/ASCII_MSDataCreation/ASCII_1.txt
MSeasy/inst/doc/Agilent_MSDataCreation
MSeasy/inst/doc/Agilent_MSDataCreation/Agilent2.D
MSeasy/inst/doc/Agilent_MSDataCreation/Agilent2.D/rteres.txt
MSeasy/inst/doc/Agilent_MSDataCreation/Agilent1.D
MSeasy/inst/doc/Agilent_MSDataCreation/Agilent1.D/rteres.txt
MSeasy/inst/CITATION
MSeasy/DESCRIPTION
MSeasy/data
MSeasy/data/Data_testclust.rda
MSeasy/data/ASCII_MSclust.rda
MSeasy/data/Agilent_quantT_MSclust.rda
MSeasy/data/Agilent_quantF_MSclust.rda
MSeasy/ChangeLog