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 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.

Installation

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

install.packages("enviGCMS")

or the current development snapshot from this GitHub repository:

devtools::install_github("yufree/enviGCMS")

Usage

  • 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
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.

News

Reference manual

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install.packages("enviGCMS")

0.5.0 by Miao YU, 25 days ago


https://github.com/yufree/enviGCMS


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


Authors: Miao YU [aut, cre] (<https://orcid.org/0000-0002-2804-6014>)


Documentation:   PDF Manual  


GPL-2 license


Imports xcms, MSnbase, rcdk, RColorBrewer, mixtools, BiocParallel, genefilter, grDevices, graphics, stats, utils, methods, reshape2, animation, rmarkdown, shiny, broom

Suggests knitr, testthat


See at CRAN