Learn R Programming

Metab (version 1.6.0)

Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.

Description

Metab is an R package for high-throughput processing of metabolomics data analysed by the Automated Mass Spectral Deconvolution and Identification System (AMDIS) (http://chemdata.nist.gov/mass-spc/amdis/downloads/). In addition, it performs statistical hypothesis test (t-test) and analysis of variance (ANOVA). Doing so, Metab considerably speed up the data mining process in metabolomics and produces better quality results. Metab was developed using interactive features, allowing users with lack of R knowledge to appreciate its functionalities.

Copy Link

Version

Version

1.6.0

License

GPL (>=2)

Maintainer

Raphael Aggio

Last Published

February 15th, 2017

Functions in Metab (1.6.0)

exampleIonLib

An example of the ionLib required by Metab.
normalizeByInternalStandard

Normalize metabolomics data sets by a specific metabolite defined as internal standard.
MetReportNames

MetReportNames cleans results obtained with the Automated Mass Spectral Deconvolution and Identification System (AMDIS).
MetReport

MetReport cleans and corrects results generated by the Automated Mass Spectral Deconvolution and Identification System (AMDIS).
buildLib

buildLib converts an AMDIS' library into a CSV file in the formated required by Metab.
exampleHtest

An example of the results obtained using the function htest.
exampleMSLfile

An example of MSL file of an AMDIS library.
htest

Function developed to apply t-test or ANOVA on a data frame.
Metab-package

Metab processes metabolomics data previously analyzed by the Automated Mass Spectral and Deconvolution System (AMDIS).
normalizeByBiomass

A function to normalize metabolomics data by the biomass associated to each biological sample (e.g. cell number or O.D.)
exampleAMDISReport

AMDIS report.
exampleBiomass

An example of the biomass data frame to be used in conjunction with the function normalizeByBiomass.
removeFalsePositives

removeFalsePositives is a function to exclude from a data frame metabolites considered false positives.
exampleMetReport

An example of the results obtained using the function exampleMetReport.