GC-MS Data Analysis for Environmental Science

Documentation for package ‘enviGCMS’ version 0.1.1

batch	Get the MIR and related information from the files
combinemd	Combine two or more matrix
comparems	substrict two GC-MS data
findline	find line of the regression model
GetIntegration	GetIntegration was mainly used for get the intergration of certain ion's chromatogram data and plot the data
Getisotopologues	Get the selected isotopologues at certain MS data
getmd	import data and return the annotated matrix for GC-MS
getsubmd	Subset the data mass spectrum of certain retention time and plot them
Integration	Just intergrate data according to fixed rt and fixed noise area
ma	filter data by average moving box
plotgroup	Plot the response group of GC-MS
plothist	plot the density of the GC-MS data with EM algorithm to seperate the data into two log normal distribution.
plotint	plot the information of intergretion
plotintslope	plot the information of intergretion
plotkms	plot the kendrick mass defect diagram
plotms	plot GC-MS data as a heatmap
plotmsrt	Plot EIC of certain m/z and return dataframe for intergration
plotrtms	Plot mass spectrum of certain retention time and return mass spectrum vector (MSP file) for NIST search
plotsms	Plot the intensity distribution of GC-MS
plotsub	Plot the backgrond of data
plott	plot GC-MS data as a heatmap for constant speed of temperature rising
plottic	Plot Total Ion Chromatogram (TIC)
qbatch	Get the MIR from the file
writeMSP	Write MSP files for NIST search