Man pages for lmbramer/fticRanalysis
Analysis and visualization tools for FT-MS data
| applyFilt | Apply an S3 filter object to an ftmsData or CoreMSData S3... |
| as.compoundData | Convert Data to compoundData Class |
| as.CoreMSData | Create CoreMSData Object |
| as.moduleData | Convert Data to moduleData Class |
| as.peakData | Convert Data to peakData Class |
| as.reactionData | Convert Data to reactionData Class |
| 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 |
| calc_aroma | Calculate Aromaticity and Modified Aromaticity Values |
| calc_dbe | Calculate DBE and DBE-O Values |
| calc_element_ratios | Calculate Elemental Ratios |
| calc_gibbs | Calculate Cox Gibbs Free Energy |
| calc_kendrick | Calculate Kendrick Mass and Defect |
| calc_nosc | Calculate Nominal Oxidation State of Carbon (NOSC) Values |
| classesPlot | Plot to look at the percentage of each class in the data |
| combinePeaksWithSameFormula | Combine rows of an ftmsData object with the same mass formula |
| comparisonMatrix | Create a matrix of which pairwise comparisons to make |
| compound_calcs | Wrapper function to calculate values associated with... |
| concat | Combine multiple ftmsData objects |
| conf_filter | Create conf\_filter object |
| conf_filter_dt | Confidence Filter Data Table |
| coreMSDataToFtmsData | CoreMSData to ftmsData |
| densityPlot | Density plot of quantitative characteristic of peaks for a... |
| divideByGroup | Divide an ftmsData object by group to form a list of ftmsData... |
| divideByGroupComparisons | Construct a list of group comparisons |
| divideBySample | Divide an ftmsData objecdt by sample to form a list |
| edata_replace | Replace Values Equal to x with y |
| edata_transform | Apply a Transformation to the Data |
| emeta_filter | Create e\_meta filter object |
| examplePeakData | FTICR Data Object of Class peakData |
| exampleProcessedPeakData | Processed FTICR Data Object of Class peakData |
| filter_worker | Remove items that need to be filtered out |
| formula_filter | Formula filter object |
| ftms12T_edata | FTICR Expression Data |
| ftms12T_emeta | FTICR Peak Meta Information |
| ftms12T_fdata | FTICR Sample Feature Data |
| 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 |
| getDatabase | Get database associated with an ftmsData object |
| getDataScale | Get data scale |
| 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... |
| 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 |
| getGroupComparisonSummaryFunctionNames | Group comparison summary functions |
| getGroupDF | Get group_DF attribute from ftmsData object |
| getGroupSummaryFunctionNames | Group summary functions |
| getHCRatioColName | Get the name of the H:C ratio column |
| getHydrogenColName | Get the name of the hydrogen column |
| getInstrumentType | Get instrument_type attribute from ftmsData object |
| 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 |
| getMassColName | Get the name of the mass column |
| getMFColName | Get the name of the e_meta unique identifier column |
| getMFNameColName | Get the name of the mf name/description column |
| getModAromaColName | Get the name of the modified aromaticity column |
| getModuleColName | Get the name of the module column |
| getModuleName | Get module name |
| getModuleNodeColName | Get the name of the module column |
| getNCRatioColName | Get the name of the N:C ratio column |
| getNitrogenColName | Get the name of the nitrogen column |
| getNOSCColName | Get the name of the NOSC column |
| getNPRatioColName | Get the name of the N:P ratio 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 |
| getPrincipalCoordinates | Get principal coordinates for the samples in an ftmsData... |
| getRatioColName | Get the name of a ratio column |
| getReactionColName | Get the name of the reaction column |
| getSulfurColName | Get the name of the sulfur column |
| getVanKrevelenCategoryBounds | Get Van Krevelen category bounds for a boundary set |
| group_designation | Creates Data Frame for Group Membership Based on Specified... |
| gtest.standard | G-test function |
| heatmap | Heatmap of density of high resolution data |
| kendrickPlot | Kendrick plot of an ftmsData object |
| mapCompoundsToModules | Map compound level data to modules in MetaCyc |
| mapCompoundsToReactions | Map compound level data to reactions in MetaCyc |
| mapPeaksToCompounds | Map peak FT-MS data to compounds |
| mass_error_plot | Generates mass-error plot for CoreMS output data |
| mass_filter | Filter Data Based on Mass Range |
| molecule_filter | Molecule filter object |
| numPeaksPlot | Plot to look at the number of peaks per sample |
| one_factor_change | Create a list of which pairwise comparisons to make |
| parse_mf | Parse Molecular Formulae to Obtain Elemental Counts |
| parseModuleReaction | Parse module reaction string |
| pipe | Pipe operator |
| plot.confFilt | Plot confidence filter object |
| plot.CoreMSData | Plot Method for CoreMSData Objects |
| plot.emetaFilt | Default plot method for emetaFilt |
| plot.formulaFilt | Plot formula filter |
| plotlyHeatmap | A wrapper of the plot_ly function to create a heatmap |
| plot.massFilt | Plot mass filter object |
| plot.moleculeFilt | Plot molecule filter data |
| plot.peakData | Plot method for peakData objects |
| plotPrincipalCoordinates | Plot principal coordinates of ftmsData samples |
| read_CoreMS_data | Read in CoreMS output |
| scatterPlot | Scatter Plot |
| setAromaColName | Set the name of the aromaticity column |
| setBS1ColName | Set the name of the peak class column based on boundary set 1 |
| setBS2ColName | Set the name of the peak class column based on boundary set 2 |
| setBS3ColName | Set the name of the peak class column based on boundary set 3 |
| setCarbonColName | Set the name of the carbon column |
| setCompoundColName | Set the name of the compound column |
| setDBEAIColName | Set the name of the double-bond equivalent AI column |
| setDBEColName | Set the name of the double-bond equivalent column |
| setDBEoColName | Set the name of the double-bond equivalent minus oxygen... |
| setDBEValenceDF | Set the valence_DF attribute |
| setEDataColName | Set the name of the e_data unique identifier column |
| setElCompColName | Set the name of the elemental composition column |
| setElementColName | Set the name of the column of the specified element |
| setExtractionColName | Set the name of the extraction column |
| setFDataColName | Set the name of the f_data unique identifier column |
| setGibbsColName | Set the name of the gibbs free energy column |
| setHCRatioColName | Set the name of the H:C ratio column |
| setHydrogenColName | Set the name of the hydrogen column |
| setIsotopicColName | Set the name of the isotopic column |
| setKendrickDefectColName | Set the names of the Kendrick defect column |
| setKendrickMassColName | Set the name of the Kendrick mass column |
| setMassColName | Set the name of the mass column |
| setMFColName | Set the name of the e_meta unique identifier column |
| setMFNameColName | Set the name of the mf name/description column |
| setModAromaColName | Set the name of the modified aromaticity column |
| setModuleColName | Set the name of the module column |
| setModuleNodeColName | Set the name of the module node column |
| setNCRatioColName | Set the name of the N:C ratio column |
| setNitrogenColName | Set the name of the nitrogen column |
| setNOSCColName | Set the name of the NOSC column |
| setNPRatioColName | Set the name of the N:P ratio column |
| setOCRatioColName | Set the name of the O:C ratio column |
| setOxygenColName | Set the name of the oxygen column |
| setPCRatioColName | Set the name of the P:C ratio column |
| setPhosphorusColName | Set the name of the phosphorus column |
| setRatioColName | Set the name of the specified ratio column |
| setReactionColName | Set the name of the reaction column |
| setSulfurColName | Set the name of the sulfur column |
| subset | Subset an ftmsData object according to sample or group |
| summarizeGroupComparisons | Summarize group comparisons |
| summarizeGroups | Summarize samples to group level estimates |
| summary.emetaFilt | Summary method for emetaFilt object |
| summary.formulaFilt | Summary method for formulaFilt object |
| summary.ftmsData | Summary of an ftmsData object |
| summary.massFilt | Summary method for massFilt object |
| summary.moleculeFilt | Summary method for moleculeFilt object |
| transformation_counts | Calculate and Count Observed Mass Transformations |
| unique_mf_assignment | Unique Molecular Formula Assignment |
| 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 |
| vanKrevelenPlot | Van Krevelen plot of an ftmsData object |
| vector_replace | Replace x with y for a single vector |
| vignette_interactivity_between_plots | Vignette: Interactivity Between Plotly Plots |
