MSP                     MSP-class
NDP                     Calculate the normalised dot product
[                       Extract parts of a 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
combine                 combine method for MSP class
compartmentTissue       Example data for 'MetCirc': 'compartmentTissue'
convert2MSP             Convert deconvoluted matrix into MSP format
convertExampleDF        Example data for 'MetCirc': convertExampleDF
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 LinkMatrix
cutUniquePreMZ          Get unique precursor ions
getBegEndIndMSP         Get beginning and end indices of each entry in
                        a data.frame in msp format
getLinkMatrixIndices    Get indices in LinkMatrix of feature
getMSP                  getMSP method for MSP class
getMetaboliteClass      getMetaboliteClass returns names of compounds
                        in MSP object
getMetaboliteName       getMetaboliteName returns names of metabolites
                        in MSP object
getName                 getName returns names in MSP object
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'
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
plotCircos              Circular plot to visualise similarity
printInformationHover   Display information on connected features of
                        hovered features
sd01_outputXCMS         Example data for 'MetCirc': 'sd01_outputXCMS'
sd02_deconvoluted       Example data for 'MetCirc': sd02_deconvoluted
setMetaboliteClass      setMetaboliteClass sets class names of
                        compounds in MSP objects
setMetaboliteName       setMetaboliteName sets metabolite names in MSP
                        objects
setName                 setName sets names in MSP objects
shinyCircos             Interactive visualisation of similar precursors
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
