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enviGCMS: GC-MS Data Analysis for Environmental Science

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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.