Package index • MetFamily

All functions

addSiriusAnnotations(): Add Sirius Annotations

add_qfeatures(): Add qfeatures to dataList

analyzeTree(): Analyze tree

calcPlotDendrogram(): Prepare dendrogram plot

calcPlotDendrogram_plotly(): Prepare Dendrogram for Plotly

calcPlotHeatmap(): Plot Heatmap

calcPlotHeatmapLegend(): Prep Heatmap Legend

calcPlotMS2(): MS2 Plot

calcPlotMS2Legend(): MS2 plot legend

calcPlotPCAloadings(): PCA plot of loadings

calcPlotPCAscores(): PCA plot of samples

calculateCluster(): Create cluster object

calculateDistanceMatrix(): Calculate a distance matrix between MS/MS spectra in the MetFamily feature Matrix

calculatePCA(): Calculate PCA

castListEntries(): Cast logical's and numeric's in a list or data.frame

colorPaletteScores(): Colors

convertToProjectFile(): Convert to Project File

data.numericmatrix(): Convert data.frame columns to numeric

filterData(): Filter a dataList

filterLFC(): Filter dataset based on LFC of two groups

filterThreshold(): Filter dataset based on intensity mean values

getAvailableClassifiers(): Classifiers

getPrecursorColors(): Create annotation colors

importParameterSetInit(): Default values

makeFilterObj(): Create a filterObject for console use

metaboliteFamilyVersusClass(): Title

mzClustGeneric(): Alignment of high resolution mass spectra

parameterSetDefault(): Create a parameterSet object

parseMSP_attributes(): parseMSP_attributes

parsePeakAbundanceMatrixQF(): Title

performPca(): Run PCA

processMS1data(): Process MS-Dial-like MS1 data.frame

projectFromFiles(): Create a project dataList

readClusterDataFromProjectFile(): Read MetFamily Project data saved by the export function

readMSDial(): Read MS-DIAL Output File into a QFeatures Object

readMetaboscape(): Read Metaboscape Output File into a QFeatures Object

readProjectData(): Read MetFamily Project data saved by the export function

runMetFamily(): Start the web app in browser

sparseMatrixToString(): Flatten listObject to string for export

swap_names_and_values(): Swap a vector's names and values