GC/LC-MS Data Analysis for Environmental Science

Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.

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enviGCMS provides functions for GC/LC-MS data analysis for environmental sciences.


You can either use the stable version of enviGCMS from CRAN,


or the current development snapshot from this GitHub repository:



  • get the mean and RSD of one sample for 5 technique replicate
data1 <- getmd(‘sample1-1’)
data2 <- getmd(‘sample1-2’)
data3 <- getmd(‘sample1-3’)
data4 <- getmd(‘sample1-4’)
data5 <- getmd(‘sample1-5’)
  • get the mean
data <- (data1+data2+data3+data4+data5)/5
  • get the standard deviation
datasd <- sqrt(((data1-data)^2+(data2-data)^2+(data3-data)^2+(data4-data)^2+(data5-data)^2)/4)
  • get the RSD
databrsd <- datasd/data
  • plot the smooth scatter
  • plot the heatmap
  • plot the mz-rt scatter plot
  • plot the boundary model

Detailed usage of those functions in Environmental analysis could be found in this paper and the vignettes in this package.


enviGCMS 0.5.0

  • CRAN

Major changes from last CRAN version 0.3.4

  • use list to communicate results between function instead of xcms objects
  • getdoe function to handle data for various experimental design
  • add functions and shiny application for Short-Chain Chlorinated Paraffins analysis
  • update the visulization function
  • support xcms 3 new objects

enviGCMS 0.4.5

Major changes

  • remove GlobalStd function and shiny application into pmd package
  • remove batch correction and simulation function into mzrtsim package
  • add shiny application for sccp analysis
  • add deprecated function
  • update vignettes

enviGCMS 0.4.4

Major changes

  • Shiny application for GlobalStd
  • New GlobalStd algorithm
  • New paired analysis based on retention time hierarchical clustering, paired mass differences(PMD), PMD frequency analysis
  • Remove mass defect related analysis
  • Plot function for paired analysis
  • Plot function for GlobalStd result
  • Organize the codes

Minor changes

  • Add Mode function
  • reformate code by formatR package

enviGCMS 0.4.3

Major changes

  • RT cluster analysis for tentative isotope, adducts, and neutral loss peaks detection
  • Correlation analysis to select the feature peaks within rt groups
  • Mass defect(cluster) analysis for homologous series detection
  • Add csv file generation for simulation data
  • Add heatmap for mzrt profile
  • Add index to plotpca

Minor changes

  • Fit xcms 3 new function in getdata2
  • Change the default name for metaboanalyst
  • remove nonascll in CITATION
  • remove faahKO package and MSnbase version for cran check

enviGCMS 0.4.2

Major changes

  • update Vignette
  • add function for SCCP analysis
  • add peak list filter function based mass difference

Minor changes

  • add seealso

enviGCMS 0.4.1

Major changes

  • add batch correction methods with p-value and q-value: sva, isva
  • remove svadata and svaupload
  • add mzrtsim to simulate mzrt profile
  • add simmzrt to make simulation input data
  • add rlaplot and ridagesplot to show the distribution of the data

Minor changes

  • revise citation keywords

enviGCMS 0.4.0

Major changes

  • Add getdoe and remove former DoE related function
  • Change the plot function from xcmsset based to list based
  • Add support for xcms 3 function


Reference manual

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0.6.0 by Miao YU, 2 months ago


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

Authors: Miao YU [aut, cre] , Thanh Wang [ctb]

Documentation:   PDF Manual  

GPL-2 license

Imports Rdisop, RColorBrewer, mixtools, BiocParallel, genefilter, grDevices, graphics, stats, utils, methods, reshape2, animation, data.table, rmarkdown, shiny, shinythemes, DT, crosstalk, dplyr, plotly, broom, igraph, ggraph, ggplot2, ggridges

Suggests knitr, testthat, xcms, MSnbase

Suggested by pmd.

See at CRAN