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 as raw data process, molecular isotope ratio, matrix effects, batch correction, mass defect filter, 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.


Reference manual

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0.3.4 by Miao YU, 8 months ago


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

Authors: Miao YU [aut, cre]

Documentation:   PDF Manual  

GPL-2 license

Imports xcms, rcdk, RColorBrewer, limma, qvalue, sva, mixtools, BiocParallel, genefilter, grDevices, graphics, stats, utils

Suggests knitr, rmarkdown, faahKO

See at CRAN