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

enviGCMS 0.5.0

  • CRAN

Major changes from last CRAN version 0.3.4

  • use list to communicate results between function instead of xcms objects
  • getdoe function to handle data for various experimental design
  • add functions and shiny application for Short-Chain Chlorinated Paraffins analysis
  • update the visulization function
  • support xcms 3 new objects

enviGCMS 0.4.5

Major changes

  • remove GlobalStd function and shiny application into pmd package
  • remove batch correction and simulation function into mzrtsim package
  • add shiny application for sccp analysis
  • add deprecated function
  • update vignettes

enviGCMS 0.4.4

Major changes

  • Shiny application for GlobalStd
  • New GlobalStd algorithm
  • New paired analysis based on retention time hierarchical clustering, paired mass differences(PMD), PMD frequency analysis
  • Remove mass defect related analysis
  • Plot function for paired analysis
  • Plot function for GlobalStd result
  • Organize the codes

Minor changes

  • Add Mode function
  • reformate code by formatR package

enviGCMS 0.4.3

Major changes

  • RT cluster analysis for tentative isotope, adducts, and neutral loss peaks detection
  • Correlation analysis to select the feature peaks within rt groups
  • Mass defect(cluster) analysis for homologous series detection
  • Add csv file generation for simulation data
  • Add heatmap for mzrt profile
  • Add index to plotpca

Minor changes

  • Fit xcms 3 new function in getdata2
  • Change the default name for metaboanalyst
  • remove nonascll in CITATION
  • remove faahKO package and MSnbase version for cran check

enviGCMS 0.4.2

Major changes

  • update Vignette
  • add function for SCCP analysis
  • add peak list filter function based mass difference

Minor changes

  • add seealso

enviGCMS 0.4.1

Major changes

  • add batch correction methods with p-value and q-value: sva, isva
  • remove svadata and svaupload
  • add mzrtsim to simulate mzrt profile
  • add simmzrt to make simulation input data
  • add rlaplot and ridagesplot to show the distribution of the data

Minor changes

  • revise citation keywords

enviGCMS 0.4.0

Major changes

  • Add getdoe and remove former DoE related function
  • Change the plot function from xcmsset based to list based
  • Add support for xcms 3 function

Tips

Reference manual

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install.packages("enviGCMS")

0.5.0 by Miao YU, a year ago


https://github.com/yufree/enviGCMS


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


Authors: Miao YU [aut, cre]


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


Suggested by pmd.


See at CRAN