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_pkgdown.yml
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_pkgdown.yml
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template:
params:
bootswatch: cosmo
#title: FT-MS Data Analysis in R
home:
# strip_header: true
links:
- text: Learn more
href: https://msc-viz.emsl.pnnl.gov
navbar:
structure:
left: [home, intro, reference, articles, news]
right: github
reference:
- title: ftmsData object construction
desc: Functions to construct an ftmsData object
contents:
- '`as.compoundData`'
- '`as.moduleData`'
- '`as.peakData`'
- '`as.reactionData`'
- '`subset.peakData`'
- '`summary.ftmsData`'
- title: Meta data calculation
desc: Functions to calculate meta-data fields
contents:
- '`compound_calcs`'
- '`assign_class`'
- '`assign_elemental_composition`'
- '`assign_mf`'
- title: Filtering
desc: Functions to filter
contents:
- '`applyFilt`'
- '`mass_filter`'
- '`molecule_filter`'
- '`formula_filter`'
- '`emeta_filter`'
- '`plot.formulaFilt`'
- '`plot.massFilt`'
- '`plot.moleculeFilt`'
- '`plot.emetaFilt`'
- '`summary.formulaFilt`'
- '`summary.massFilt`'
- '`summary.moleculeFilt`'
- '`summary.emetaFilt`'
- title: Data transformation
desc: Functions to transform data (e.g. scale)
contents:
- '`edata_replace`'
- '`edata_transform`'
- title: Treatment groups and group comparisons
desc: Defining experimental groups and comparisons
contents:
- '`group_designation`'
- '`comparisonMatrix`'
- '`concat`'
- '`divideByGroup`'
- '`summarizeGroups`'
- '`divideByGroupComparisons`'
- '`divideBySample`'
- '`summarizeGroupComparisons`'
- '`uniqueness_gtest`'
- '`uniqueness_nsamps`'
- '`uniqueness_prop`'
- title: Visualization
desc: Visualization methods
contents:
- '`plot.peakData`'
- '`classesPlot`'
- '`densityPlot`'
- '`kendrickPlot`'
- '`vanKrevelenPlot`'
- '`scatterPlot`'
- '`plotPrincipalCoordinates`'
- '`vignette_interactivity_between_plots`'
- '`panelFunctionGenerator`'
- '`densityCognostics`'
- '`kendrickCognostics`'
- '`vanKrevelenCognostics`'
- title: Database mapping
desc: Functions to map to biological databases
contents:
- '`mapPeaksToCompounds`'
- '`mapCompoundsToReactions`'
- '`mapCompoundsToModules`'
- '`parseModuleReaction`'
- '`combinePeaksWithSameFormula`'
# - '`plotReactionGraph`'
# - '`plotlyHeatmap`'
- title: Convenience methods
desc: ~
contents:
- '`getDataScale`'
- '`getDatabase`'
- '`getGroupDF`'
- '`getGroupSummaryFunctionNames`'
- '`getInstrumentType`'
- '`getModuleName`'
- '`getVanKrevelenCategoryBounds`'
- title: CoreMS to ftmsRanalysis conversion
contents:
- 'coreMSDataToFtmsData'
- 'as.CoreMSData'
- title: Column name methods
desc: Methods to get the column name used to store various meta data values
contents:
- '`getAromaColName`'
- '`getBS1ColName`'
- '`getBS2ColName`'
- '`getBS3ColName`'
- '`getCarbonColName`'
- '`getCompoundColName`'
- '`getDBEAIColName`'
- '`getDBEColName`'
- '`getDBEoColName`'
- '`getEDataColName`'
- '`getElCompColName`'
- '`getElementColName`'
- '`getExtractionColName`'
- '`getFDataColName`'
- '`getGibbsColName`'
- '`getHCRatioColName`'
- '`getHydrogenColName`'
- '`getIsotopicColName`'
- '`getKendrickDefectColName`'
- '`getKendrickMassColName`'
- '`getMFColName`'
- '`getMFNameColName`'
- '`getMassColName`'
- '`getModAromaColName`'
- '`getModuleColName`'
- '`getModuleNodeColName`'
- '`getNCRatioColName`'
- '`getNOSCColName`'
- '`getNPRatioColName`'
- '`getNitrogenColName`'
- '`getOCRatioColName`'
- '`getOxygenColName`'
- '`getPCRatioColName`'
- '`getPhosphorusColName`'
- '`getRatioColName`'
- '`getReactionColName`'
- '`getSulfurColName`'
- title: Example data objects
desc: Example data included in the `ftmsRanalysis` package
contents:
- '`examplePeakData`'
- '`exampleProcessedPeakData`'
- '`ftms12T_edata`'
- '`ftms12T_emeta`'
- '`ftms12T_fdata`'
- title: internal
desc: Other functions
contents:
- calc_aroma
- calc_dbe
- calc_element_ratios
- calc_gibbs
- calc_kendrick
- calc_nosc
- conf_filter
- conf_filter_dt
- filter_worker
- getGroupComparisonSummaryFunctionNames
- getPrincipalCoordinates
- gtest.standard
- heatmap
- mass_error_plot
- numPeaksPlot
- one_factor_change
- parse_mf
- plot.CoreMSData
- plot.confFilt
- plotlyHeatmap
- read_CoreMS_data
- setAromaColName
- setBS1ColName
- setBS2ColName
- setBS3ColName
- setCarbonColName
- setCompoundColName
- setDBEAIColName
- setDBEColName
- setDBEValenceDF
- setDBEoColName
- setEDataColName
- setElCompColName
- setElementColName
- setExtractionColName
- setFDataColName
- setGibbsColName
- setHCRatioColName
- setHydrogenColName
- setIsotopicColName
- setKendrickDefectColName
- setKendrickMassColName
- setMFColName
- setMFNameColName
- setMassColName
- setModAromaColName
- setModuleColName
- setModuleNodeColName
- setNCRatioColName
- setNOSCColName
- setNPRatioColName
- setNitrogenColName
- setOCRatioColName
- setOxygenColName
- setPCRatioColName
- setPhosphorusColName
- setRatioColName
- setReactionColName
- setSulfurColName
- transformation_counts
- unique_mf_assignment
- vector_replace
github:
- icon: fa-github
href: https://github.com/EMSL-Computing