Function reference • ftmsRanalysis

ftmsData object construction Functions to construct an ftmsData object
`as.compoundData()`	Convert Data to compoundData Class
`as.moduleData()`	Convert Data to moduleData Class
`as.peakData()`	Convert Data to peakData Class
`as.reactionData()`	Convert Data to reactionData Class
`subset(<peakData>)` `subset(<compoundData>)` `subset(<reactionData>)` `subset(<moduleData>)`	Subset an ftmsData object according to sample or group
`summary(<ftmsData>)`	Summary of an ftmsData object
Meta data calculation Functions to calculate meta-data fields
`compound_calcs()`	Wrapper function to calculate values associated with individual peaks/compounds
`assign_class()`	Assign compound class to each peak/mass
`assign_elemental_composition()`	Assign elemental composition to each peak/mass
`assign_mf()`	Assign Molecular Formulae Based on Element Counts
Filtering Functions to filter
`applyFilt()`	Apply an S3 filter object to an ftmsData or CoreMSData S3 object
`mass_filter()`	Filter Data Based on Mass Range
`molecule_filter()`	Molecule filter object
`formula_filter()`	Formula filter object
`emeta_filter()`	Create e\_meta filter object
`plot(<formulaFilt>)`	Plot formula filter
`plot(<massFilt>)`	Plot mass filter object
`plot(<moleculeFilt>)`	Plot molecule filter data
`plot(<emetaFilt>)`	Default plot method for emetaFilt
`summary(<formulaFilt>)`	Summary method for formulaFilt object
`summary(<massFilt>)`	Summary method for massFilt object
`summary(<moleculeFilt>)`	Summary method for moleculeFilt object
`summary(<emetaFilt>)`	Summary method for emetaFilt object
Data transformation Functions to transform data (e.g. scale)
`edata_replace()`	Replace Values Equal to x with y
`edata_transform()`	Apply a Transformation to the Data
Treatment groups and group comparisons Defining experimental groups and comparisons
`group_designation()`	Creates Data Frame for Group Membership Based on Specified Main Effects
`comparisonMatrix()`	Create a matrix of which pairwise comparisons to make
`concat()`	Combine multiple distributed data objects of ftmsData
`divideByGroup()`	Divide an ftmsData object by group to form a ddo
`summarizeGroups()`	Summarize samples to group level estimates
`divideByGroupComparisons()`	Construct a ddo of group comparisons
`divideBySample()`	Divide an ftmsData objecdt by sample to form a ddo
`summarizeGroupComparisons()`	Summarize group comparisons
`uniqueness_gtest()`	Determine Unique and Common Masses Between Two Groups
`uniqueness_nsamps()`	Determine Unique and Common Masses/Peaks for Two Groups
`uniqueness_prop()`	Determine Unique and Common Masses/Peaks for Two Groups
Visualization Visualization methods
`plot(<peakData>)`	Plot method for peakData objects
`classesPlot()`	Plot to look at the percentage of each class in the data
`densityPlot()`	Density plot of quantitative characteristic of peaks for a peakData or compoundData object
`kendrickPlot()`	Kendrick plot of an ftmsData object
`vanKrevelenPlot()`	Van Krevelen plot of an ftmsData object
`scatterPlot()`	Scatter Plot
`plotPrincipalCoordinates()`	Plot principal coordinates of ftmsData samples
`vignette_interactivity_between_plots`	Vignette: Interactivity Between Plotly Plots
`panelFunctionGenerator()`	Convenience function to wrap ftmsRanalysis plotting functions for Trelliscope
`densityCognostics()`	Default cognostics for density plots in Trelliscope
`kendrickCognostics()`	Default cognostics for Kendrick plots in Trelliscope
`vanKrevelenCognostics()`	Default cognostics for Van Krevelen plots in Trelliscope
Database mapping Functions to map to biological databases
`mapPeaksToCompounds()`	Map peak FT-MS data to compounds
`mapCompoundsToReactions()`	Map compound level data to reactions in MetaCyc
`mapCompoundsToModules()`	Map compound level data to modules in MetaCyc
`parseModuleReaction()`	Parse module reaction string
`combinePeaksWithSameFormula()`	Combine rows of an ftmsData object with the same mass formula
Convenience methods
`getDataScale()`	Get data scale
`getDatabase()`	Get database associated with an ftmsData object
`getGroupDF()`	Get group_DF attribute from ftmsData object
`getGroupSummaryFunctionNames()`	Group summary functions
`getInstrumentType()`	Get instrument_type attribute from ftmsData object
`getModuleName()`	Get module name
`getVanKrevelenCategoryBounds()`	Get Van Krevelen category bounds for a boundary set
CoreMS to ftmsRanalysis conversion
`coreMSDataToFtmsData()`	CoreMSData to ftmsData
`as.CoreMSData()`	Create CoreMSData Object
Column name methods Methods to get the column name used to store various meta data values
`getAromaColName()`	Get the name of the aromaticity column
`getBS1ColName()`	Get the name of the peak class column based on boundary set 1
`getBS2ColName()`	Get the name of the peak class column based on boundary set 2
`getBS3ColName()`	Get the name of the peak class column based on boundary set 3
`getCarbonColName()`	Get the name of the carbon column
`getCompoundColName()`	Get the name of the compound column
`getDBEAIColName()`	Get the name of the double-bond equivalent AI column
`getDBEColName()`	Get the name of the double-bond equivalent column
`getDBEoColName()`	Get the name of the double-bond equivalent minus oxygen column
`getEDataColName()`	Get the name of the e_data unique identifier column
`getElCompColName()`	Get the name of the elemental composition column
`getElementColName()`	Get the name of the column for the specified element
`getExtractionColName()`	Get the name of the extraction column
`getFDataColName()`	Get the name of the f_data unique identifier column
`getGibbsColName()`	Get the name of the gibbs free energy column
`getHCRatioColName()`	Get the name of the H:C ratio column
`getHydrogenColName()`	Get the name of the hydrogen column
`getIsotopicColName()`	Get the name of the isotopic column
`getKendrickDefectColName()`	Get the names of the Kendrick defect column
`getKendrickMassColName()`	Get the name of the Kendrick mass column
`getMFColName()`	Get the name of the e_meta unique identifier column
`getMFNameColName()`	Get the name of the mf name/description column
`getMassColName()`	Get the name of the mass column
`getModAromaColName()`	Get the name of the modified aromaticity column
`getModuleColName()`	Get the name of the module column
`getModuleNodeColName()`	Get the name of the module column
`getNCRatioColName()`	Get the name of the N:C ratio column
`getNOSCColName()`	Get the name of the NOSC column
`getNPRatioColName()`	Get the name of the N:P ratio column
`getNitrogenColName()`	Get the name of the nitrogen column
`getOCRatioColName()`	Get the name of the O:C ratio column
`getOxygenColName()`	Get the name of the oxygen column
`getPCRatioColName()`	Get the name of the P:C ratio column
`getPhosphorusColName()`	Get the name of the phosphorus column
`getRatioColName()`	Get the name of a ratio column
`getReactionColName()`	Get the name of the reaction column
`getSulfurColName()`	Get the name of the sulfur column
Example data objects Example data included in the `ftmsRanalysis` package
`examplePeakData`	FTICR Data Object of Class peakData
`exampleProcessedPeakData`	Processed FTICR Data Object of Class peakData
`ftms12T_edata`	FTICR Expression Data
`ftms12T_emeta`	FTICR Peak Meta Information
`ftms12T_fdata`	FTICR Sample Feature Data

Reference

ftmsData object construction

Meta data calculation

Filtering

Data transformation

Treatment groups and group comparisons

Visualization

Database mapping

Convenience methods

CoreMS to ftmsRanalysis conversion

Column name methods

Example data objects