GC/LC-MS Data Analysis for Environmental Science

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Documentation for package ‘enviGCMS’ version 0.9.0

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c.mzrt c method for mzrt object
cleanMGF Clean an MGF file by keeping only formula-explainable peaks
findline find line of the regression model for GC-MS
findlipid Find lipid class of metabolites base on referenced Kendrick mass defect
findmet Screen metabolites by Mass Defect
findohc Screen organohalogen compounds by retention time, mass defect analysis and isotope relationship modified by literature report. Also support compounds with [M] and [M+2] ratio cutoff.
findpfc Find PFCs based on mass defect analysis
getalign Align two peaks vectors by mass to charge ratio and/or retention time
getalign2 Align mass to charge ratio and/or retention time to remove redundancy
getcompare Align multiple peaks list to one peak list
getcsv Convert an list object to csv file.
getdoe Generate the group level rsd and average intensity based on DoE,
getdwtus Density weighted intensity for one sample
getfilter Filter the data based on row and column index
getformula Get chemical formula for mass to charge ratio.
getHRMF Batch High Resolution Mass Filtering for all compounds in an MSP file
getimputation Impute the peaks list data
getintegration getintegration was mainly used for get the integration of certain ion's chromatogram data and plot the data
getisotopologues Get the selected isotopologues at certain MS data
getmass Get the exact mass of the isotopologues from a chemical formula or reaction's isotope patterns with the highest abundances
getmassdefect Get mass defect with certain scaled factor
getmdh Get the high order unit based Mass Defect
getmdr Get the raw Mass Defect
getms1anno Annotation of MS1 data by compounds database by predefined paired mass distance
getMSP read in MSP file as list for ms/ms or ms(EI) annotation
getmzrtcsv Covert the peaks list csv file into list
getoverlappeak Get the overlap peaks by mass and retention time range
getpn Merge positive and negative mode data
getpower Get the index with power restriction for certain study with BH adjusted p-value and certain power.
getpqsi Compute pooled QC linear index according to run order
getrangecsv Get a mzrt list and/or save mz and rt range as csv file.
getretcor Perform peaks list alignment and return features table
getrmd Get the Relative Mass Defect
gifmr plot scatter plot for rt-mz profile and output gif file for multiple groups
HRMF High Resolution Mass Filtering (HRMF) for GC/LC HRMS data
integration Just integrate data according to fixed rt and fixed noise area
list Demo data
ma filter data by average moving box
matrix Demo raw data matrix
plotcc plot the calibration curve with error bar, r squared and equation.
plotden plot the density for multiple samples
plotdwtus plot density weighted intensity for multiple samples
plotEIC Plot extracted ion chromatograms from raw mzML/mzXML data
plotgroup Plot the response group of GC-MS
plothist plot the density of the GC-MS data with EM algorithm to separate the data into two log normal distribution.
plothm Plot the heatmap of mzrt profiles
plotint plot the information of integration
plotintslope plot the slope information of integration
plotkms plot the kendrick mass defect diagram
plotmr plot the scatter plot for peaks list with threshold
plotmrc plot the diff scatter plot for peaks list with threshold between two groups
plotms plot GC/LC-MS data as a heatmap with TIC
plotmz plot GC/LC-MS data as scatter plot
plotpca plot the PCA for multiple samples
plotpeak plot intensity of peaks across samples or samples across peaks
plotridge plot ridgeline density plot
plotridges Relative Log Abundance Ridge (RLAR) plots for samples or peaks
plotrla Relative Log Abundance (RLA) plots
plotrsd plot the rsd influences of data in different groups
plotrug plot 1-d density for multiple samples
plotsms Plot the intensity distribution of GC-MS
plotsub Plot the background of data
plott plot GC-MS data as a heatmap for constant speed of temperature rising
plottic Plot Total Ion Chromatogram (TIC)
plotTopMS1Peaks Extract top MS1 ions from MS2 EIC interactively
plotTopMS2Peaks Extract top MS2 ions from MS1 EIC interactively
runMDPlot Shiny application for interactive mass defect plots analysis
runsccp Shiny application for Short-Chain Chlorinated Paraffins analysis
sccp Short-Chain Chlorinated Paraffins(SCCPs) peaks information for quantitative analysis
TBBPA Demo data for TBBPA metabolism in Pumpkin
writeMSP Write MSP file for NIST search