Package index
-
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
-
cosine_similarity() - Calculate cosine/modified cosine score
-
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
-
filter_msp_entries() - Filter MSP entries
-
getAvailableClassifiers() - Classifiers
-
getPrecursorColors() - Create annotation colors
-
impl_cosine_similarity() - Implement Cosine Similarity
-
importParameterSetInit() - Default values
-
makeFilterObj() - Create a filterObject for console use
-
metaboliteFamilyVersusClass() - Title
-
mgf_dict() - MGF header dictionnary
-
msp_dict() - MSP header dictionnary
-
mzClustGeneric() - Alignment of high resolution mass spectra
-
parameterSetDefault() - Create a parameterSet object
-
parseMGF() - Read MGF files
-
parseMGF_to_list() - Process MGF from file to list of entries
-
parseMSP()superseded - Parse MS/MS spectra
-
parseMSP_chunk()superseded - parse MSP file to list
-
parseMSP_rewrite() - Read and filter MSP spectra files
-
parseMSP_to_list() - Process MSP from file to list of entries
-
parsePeakAbundanceMatrixQF() - Title
-
performPca() - Run PCA
-
processMS1data() - Process MS-Dial-like MS1 data.frame
-
process_msp_entry() - Filter single MSP entry
-
projectFromFiles() - Create a project dataList
-
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
-
readProjectFile() - 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
-
writeProjectFile() - Export MetFamily project