MSP                     MSP-class
NDP                     Calculate the normalised dot product
[                       Extract parts of a 'MSP'-object
adduct                  'adduct' returns adduct ion names of compounds
                        in 'MSP'-object
adduct<-                'adduct<-' sets adduct ion names in
                        'MSP'-object
allocatePrecursor2mz    allocatePrecursor2mz: Join two data sources
binnedMSP               Example data for 'MetCirc': 'binnedMSP'
binning                 Bin m/z values
cart2Polar              Calculate polar coordinates from cartesian
                        coordinates
circosLegend            Plot a legend for circos plot
classes                 'classes' returns class names of compounds in
                        'MSP'-object
classes<-               'classes<-' sets information in 'MSP'-object
combine                 'combine' method for 'MSP'-class
compartmentTissue       Example data for 'MetCirc': 'compartmentTissue'
convert2MSP             Convert deconvoluted matrix into 'MSP'-object
convertExampleDF        Example data for 'MetCirc': convertExampleDF
convertMSP2MSP          Convert MSP data frame into object of
                        'MSP'-class
createLink0Matrix       Create a link matrix
createLinkMatrix        Create a matrix which contains features to link
                        (indices)
createOrderedSimMat     Update colnames and rownames of a similarity
                        matrix according to order m/z, retention time
                        and clustering
createSimilarityMatrix
                        Create similarity matrix
cutLinkMatrix           Create a cut link matrix
cutUniquePrecursor      Get unique precursor ions
getBegEndIndMSP         Get beginning and end indices of each entry in
                        a 'data.frame' in 'peaks(MSP)'-objects
getLinkMatrixIndices    Get indices in LinkMatrix of feature
getPrecursorMZ          'getPrecursorMZ' returns precursor m/z values
                        of an 'MSP'-object
getRT                   'getRT' returns precursor RT values of an
                        'MSP'-object
highlight               Add links and highlight sectors
idMSMStoMSP-data        Example data for 'MetCirc': 'finalMSP'
information             'information' returns information of
                        metabolites in 'MSP'-object
information<-           'information<-' sets information in
                        'MSP'-object
length                  'length' method for 'MSP'-class
minFragCart2Polar       Calculate the nearest feature in polar
                        coordinates given cartesian coordinates
msp2FunctionalLossesMSP
                        Convert MSP to MSP with functional losses
msp2msp                 Example data for 'MetCirc': 'msp2msp'
names                   'names' returns names in 'MSP'-object
names<-                 'names<-' sets names in 'MSP'-object
peaks                   'peaks' method for 'MSP'-class
plotCircos              Circular plot to visualise similarity
printInformationSelect
                        Display information on connected features of
                        selected features
sd01_outputXCMS         Example data for 'MetCirc': 'sd01_outputXCMS'
sd02_deconvoluted       Example data for 'MetCirc': sd02_deconvoluted
shinyCircos             Interactive visualisation of similarity and
                        navigation of MS/MS features
show                    'show' method for 'MSP'-class
similarityMat           Example data for 'MetCirc': 'similarityMat'
thresholdLinkMatrix     Threshold a link matrix
tissue                  Example data for 'MetCirc': 'tissue'
truncateName            Truncate names
