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