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 Envrionmental 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.