Function reference • enviGCMS

All functions
`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
`Integration()`	Just integrate data according to fixed rt and fixed noise area
`Mode()`	define the Mode function
`TBBPA`	Demo data for TBBPA metabolism in Pumpkin
`batch()`	Get the MIR and related information from the files
`cbmd()`	Combine two data with similar retention time while different mass range
`dotpanno()`	Perform MS/MS dot product annotation for mgf file
`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
`getMSP()`	read in MSP file as list for ms/ms or ms(EI) annotation
`getQCraw()`	get the data of QC compound for a group of data
`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
`getarea()`	Get the peak information from samples for SCCPs detection
`getareastd()`	Get the peak information from SCCPs standards
`getbgremove()`	Get the peak list with blank samples' peaks removed
`getbiotechrep()`	Get the report for biological replicates.
`getcompare()`	Align multiple peaks list to one peak list
`getcsv()`	Convert an list object to csv file.
`getdata()`	Get xcmsset object in one step with optimized methods.
`getdata2()`	Get XCMSnExp object in one step from structured folder path for xcms 3.
`getdoe()`	Generate the group level rsd and average intensity based on DoE,
`getdwtus()`	Density weighted intensity for one sample
`getfeaturesanova()`	Get the features from anova, with p value, q value, rsd and power restriction
`getfeaturest()`	Get the features from t test, with p value, q value, rsd and power restriction
`getfilter()`	Filter the data based on row and column index
`getformula()`	Get chemical formula for mass to charge ratio.
`getgrouprep()`	Get the report for samples with biological and technique replicates in different groups
`getimputation()`	Impute the peaks list 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
`getmd()`	Import data and return the annotated matrix for GC/LC-MS by m/z range and retention time
`getmdh()`	Get the high order unit based Mass Defect
`getmdr()`	Get the raw Mass Defect
`getmr()`	Get the mzrt profile and group information for batch correction and plot as a list directly from path with default setting
`getms1anno()`	Annotation of MS1 data by compounds database by predefined paired mass distance
`getmzrt()`	Get the mzrt profile and group information as a mzrt list and/or save them as csv or rds for further analysis.
`getmzrt2()`	Get the mzrt profile and group information for batch correction and plot as a list for xcms 3 object
`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
`getsccp()`	Quantitative analysis for short-chain chlorinated paraffins(SCCPs)
`getsim()`	output the similarity of two dataset
`gettechrep()`	Get the report for technique replicates.
`gettimegrouprep()`	Get the time series or two factor DoE report for samples with biological and technique replicates in different groups
`getupload()`	Get the csv files from xcmsset/XCMSnExp/list object
`getupload2()`	Get the csv files to be submitted to Metaboanalyst
`getupload3()`	Get the csv files to be submitted to Metaboanalyst
`gifmr()`	plot scatter plot for rt-mz profile and output gif file for multiple groups
`list`	Demo data
`ma()`	filter data by average moving box
`plotanno()`	Show MS/MS pmd annotation result
`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
`plote()`	plot EIC and boxplot for all peaks and return diffreport
`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
`plotmsrt()`	Plot EIC of certain m/z and return dataframe for integration
`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
`plotrtms()`	Plot mass spectrum of certain retention time and return mass spectrum vector (MSP file) for NIST search
`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)
`qbatch()`	Get the MIR from the file
`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
`submd()`	Get the differences of two GC/LC-MS data
`svabatch()`	Plot the influences of DoE and Batch effects on each peaks
`svacor()`	Surrogate variable analysis(SVA) to correct the unknown batch effects
`svadata()`	Filter the data with p value and q value
`svapca()`	Principal component analysis(PCA) for SVA corrected data and raw data
`svaplot()`	Filter the data with p value and q value and show them
`svaupload()`	Get the corrected data after SVA for metabolanalyst
`writeMSP()`	Write MSP file for NIST search
`xrankanno()`	Perform MS/MS X rank annotation for mgf file

Reference

All functions