enviGCMS: GC-MS Data Analysis for Environmental Science

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

Installation

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

install.packages("enviGCMS")

or the current development snapshot from this GitHub repository:

remotes::install_github("yufree/enviGCMS")

Usage

Check this vignette for Data analysis of GC-MS and LC-MS in Environmental Science.

Check this vignette for Pooled QC analysis in Environmental Science.

  • get the mean and RSD of one sample for 5 technique replicate
# enviGCMS use functions in xcms to import the data, just type the path to your single sample
data1 <- enviGCMS:::getmd(‘sample1-1’)
data2 <- enviGCMS:::getmd(‘sample1-2’)
data3 <- enviGCMS:::getmd(‘sample1-3’)
data4 <- enviGCMS:::getmd(‘sample1-4’)
data5 <- enviGCMS:::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
plotsms(datarsd)
  • plot the heatmap
plotms(data)
  • plot the mz-rt scatter plot
plotmz(data)
  • plot the boundary model
findline(data)

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