Package index • 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
HRMF(): High Resolution Mass Filtering (HRMF) for GC/LC HRMS data
integration(): Just integrate data according to fixed rt and fixed noise area
TBBPA: Demo data for TBBPA metabolism in Pumpkin
c(<mzrt>): c method for mzrt object
checkGoldenRules(): Check Chemical Formula against Fiehn Seven Golden Rules
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
findpfc(): Find PFCs based on mass defect analysis
getHRMF(): Batch High Resolution Mass Filtering for all compounds in an MSP file
getMSP(): read in MSP file as list for ms/ms or ms(EI) annotation
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 using the HORIZON algorithm
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
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
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
list: Demo data
ma(): filter data by average moving box
matrix: Demo raw data matrix
plotEIC(): Plot extracted ion chromatograms from raw mzML/mzXML data
plotTopMS1Peaks(): Extract top MS1 ions from MS2 EIC interactively
plotTopMS2Peaks(): Extract top MS2 ions from MS1 EIC interactively
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
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)
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
scoreIsotopes(): Calculate Isotopic Pattern Similarity Scores
writeMSP(): Write MSP file for NIST search