Man pages for enviGCMS
GC/LC-MS Data Analysis for Environmental Science

batchGet the MIR and related information from the files
cbmdCombine two data with similar retention time while different...
dotpannoPerform MS/MS dot product annotation for mgf file
enviGCMS-deprecatedDeprecated functions in package 'enviGCMS'.
findlinefind line of the regression model for GC-MS
findlipidFind lipid class of metabolites base on referenced Kendrick...
findmetScreen metabolites by Mass Defect
findohcScreen organohalogen compounds by retention time, mass defect...
getareaGet the peak information from sampels for SCCPs detection
getareastdGet the peak information from SCCPs standards
getbgremoveGet the peak list with blank samples' peaks removed
getbiotechrepGet the report for biological replicates.
getcsvConvert an list object to csv file.
getdataGet xcmsset object in one step with optimized methods.
getdata2Get XCMSnExp object in one step from structured folder path...
getdoeGenerate the group level rsd and average intensity based on...
getdwtusDensity weighted intensity for one sample
getfeaturesanovaGet the features from anova, with p value, q value, rsd and...
getfeaturestGet the features from t test, with p value, q value, rsd and...
getfilterFilter the data based on row and column index
getformulaGet chemical formula for mass to charge ratio.
getgrouprepGet the report for samples with biological and technique...
getimputationImpute the peaks list data
GetIntegrationGetIntegration was mainly used for get the intergration of...
GetisotopologuesGet the selected isotopologues at certain MS data
getmassGet the exact mass of the isotopologues from a chemical...
getmassdefectGet mass defect with certain scaled factor
getmdImport data and return the annotated matrix for GC/LC-MS by...
getmdhGet the high order unit based Mass Defect
getmdrGet the raw Mass Defect
getmrGet the mzrt profile and group information for batch...
getMSPread in MSP file as list for ms/ms or ms(EI) annotation
getmzrtGet the mzrt profile and group information as a mzrt list...
getmzrt2Get the mzrt profile and group information for batch...
getmzrtcsvCovert the peaks list csv file into list
getoverlapmassGet the overlap peaks by mass range
getoverlappeakGet the overlap peaks by mass and retention time range
getoverlaprtGet the overlap peaks by retention time
getpowerGet the index with power restriction for certain study with...
getpqsiCompute pooled QC linear index according to run order
getQCrawget the data of QC compound for a group of data
getrangecsvGet a mzrt list and/or save mz and rt range as csv file.
getrmdGet the Relative Mass Defect
getsccpQuantitative analysis for short-chain chlorinated...
getsimoutput the similarity of two dataset
gettechrepGet the report for technique replicates.
gettimegrouprepGet the time series or two factor DoE report for samples with...
getuploadGet the csv files from xcmsset/XCMSnExp/list object
getupload2Get the csv files to be submitted to Metaboanalyst
getupload3Get the csv files to be submitted to Metaboanalyst
gifmrplot scatter plot for rt-mz profile and output gif file for...
IntegrationJust intergrate data according to fixed rt and fixed noise...
listDemo data
mafilter data by average moving box
Modedefine the Mode function
plotannoShow MS/MS pmd annotation result
plotccplot the calibration curve with error bar, r squared and...
plotdenplot the density for multiple samples
plotdwtusplot density weighted intensity for multiple samples
ploteplot EIC and boxplot for all peaks and return diffreport
plotgroupPlot the response group of GC-MS
plothistplot the density of the GC-MS data with EM algorithm to...
plothmPlot the heatmap of mzrt profiles
plotintplot the information of intergretion
plotintslopeplot the slope information of intergretion
plotkmsplot the kendrick mass defect diagram
plotmrplot the scatter plot for peaks list with threshold
plotmrcplot the diff scatter plot for one xcmsset objects with...
plotmsplot GC/LC-MS data as a heatmap with TIC
plotmsrtPlot EIC of certain m/z and return dataframe for intergration
plotmzplot GC/LC-MS data as scatter plot
plotpcaplot the PCA for multiple samples
plotpeakplot intensity of peaks across samples or samples across...
plotridgeplot ridgeline density plot
plotridgesRelative Log Abundance Ridge (RLAR) plots for samples or...
plotrlaRelative Log Abundance (RLA) plots
plotrsdplot the rsd influnces of data in different groups
plotrtmsPlot mass spectrum of certain retention time and return mass...
plotrugplot 1-d density for multiple samples
plotsmsPlot the intensity distribution of GC-MS
plotsubPlot the backgrond of data
plottplot GC-MS data as a heatmap for constant speed of...
plotticPlot Total Ion Chromatogram (TIC)
qbatchGet the MIR from the file
runMDPlotShiny application for interactive mass defect plots analysis
runsccpShiny application for Short-Chain Chlorinated Paraffins...
sccpShort-Chain Chlorinated Paraffins(SCCPs) peaks infomation for...
submdGet the differences of two GC/LC-MS data
svabatchPlot the influnces of DoE and Batch effects on each peaks
svacorSurrogate variable analysis(SVA) to correct the unknown batch...
svadataFilter the data with p value and q value
svapcaPrincipal component analysis(PCA) for SVA corrected data and...
svaplotFilter the data with p value and q value and show them
svauploadGet the corrected data after SVA for metabolanalyst
TBBPADemo data for TBBPA metabolism in Pumpkin
writeMSPWrite MSP files for NIST search
xrankannoPerform MS/MS X rank annotation for mgf file
enviGCMS documentation built on July 8, 2020, 5:52 p.m.