erah

Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics

Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. Outputs a table with compound names, matching scores and the integrated area of the compound for each sample. Package implementation is described in Domingo-Almenara et al. (2016) .

News

erah v1.1.0 (Release date: 2018-07-10)

  • eRah now computes Retention Index errors. Please see the Vignette for more information.
  • New feature available for processing long chromatograms with larger peaks (> 20 seconds peak width). (Thanks to Dr. P. Fuchsmann and Mr. T. Richter)
  • New feature available to allow eRah process samples with low scans per second rates.
  • Improved compatibility to import NIST library files. (Thanks to Mr. T. Richter)
  • Faster baseline removal implementation.
  • Bugs when exporting to MSP files fixed: a new parameter (alg.version) allows switching between exporting methods. (Thanks to Dr. Long and Dr. W. Zhu)

erah v1.0.5 (Release date: 2017-01-13)

  • Bug regarding analysis.time parameter now updated.
  • Golm Metabolome Database can now be imported to eRah through importGMD.
  • New function introduced: import MSP-formatted libraries to be used with eRah (Thanks to Dr. Sogin)
  • New function introduced: export spectra to CEF format for comparison with the NIST library through MassHunter interface (Thanks to Dr. Ramirez)
  • Bugs fixed when loading certain CDF and XML files (Thanks to Mr. Nguyen-Phuoc and Mr. Wilkinson)
  • Functions updated to allow compatibility with the Baitmet R package.
  • Minor bug fixes.
  • Vignette updated.

erah v1.0.4 (Release date: 2016-10-17)

  • New function included: importMSP - importation of the GMD spectra from MSP format

erah v1.0.3 (Release date: 2016-10-13)

  • Documentation updated.
  • Minor bug fixes.
  • CDF file reading function updated, to assure compatibility with different vendors equipment (Thanks to Dr. Hasler-Sheetal).

erah v1.0.2 (Release date: 2016-09-02)

  • Documentation updated.
  • New function included: export2MSP - exportation of spectra into MSP format
  • Minor bug fixes.
  • Bug with pre-processing filter order, now fixed.
  • Bug that made eRah stop when processing some chromatograms, now fixed.

erah v1.0.1 (Release date: 2016-04-22)

  • Small documentation improvements
  • Minor improvements and bug fixes.

erah v1.0.0 (Release date: 2016-04-15)

First commit.

Reference manual

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install.packages("erah")

1.1.0 by Xavier Domingo-Almenara, a year ago

http://metabolomicsplatform.com/

Browse source code at https://github.com/cran/erah

Authors: Xavier Domingo-Almenara [aut, cre, cph] , Sara Samino [aut] , Maria Vinaixa [aut] , Alexandre Perera [aut, ths] , Jesus Brezmes [aut, ths] , Oscar Yanes [aut, ths]

Documentation:   PDF Manual  

GPL (>= 2) license

Imports ncdf4, nnls, igraph, signal, quantreg, XML, methods

Depends on Rcpp

Suggests R.rsp, mzR

Depended on by baitmet.

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