adduct | 'adduct' returns adduct ion names of compounds in 'MSP'-object |
adduct-method | 'adduct' returns adduct ion names of compounds in 'MSP'-object |
adduct<- | 'adduct<-' sets adduct ion names in 'MSP'-object |
adduct<--method | '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-method | 'classes' returns class names of compounds in 'MSP'-object |
classes<- | 'classes<-' sets information in 'MSP'-object |
classes<--method | 'classes<-' sets information in 'MSP'-object |
combine | 'combine' method for 'MSP'-class |
combine-method | '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 |
finalMSP | Example data for 'MetCirc': 'finalMSP' |
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 |
getPrecursorMZ-method | 'getPrecursorMZ' returns precursor m/z values of an 'MSP'-object |
getRT | 'getRT' returns precursor RT values of an 'MSP'-object |
getRT-method | '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-method | 'information' returns information of metabolites in 'MSP'-object |
information<- | 'information<-' sets information in 'MSP'-object |
information<--method | 'information<-' sets information in 'MSP'-object |
length | 'length' method for 'MSP'-class |
length-method | 'length' method for 'MSP'-class |
minFragCart2Polar | Calculate the nearest feature in polar coordinates given cartesian coordinates |
MSP | MSP-class |
MSP-class | MSP-class |
msp2FunctionalLossesMSP | Convert MSP to MSP with functional losses |
msp2msp | Example data for 'MetCirc': 'msp2msp' |
names | 'names' returns names in 'MSP'-object |
names-method | 'names' returns names in 'MSP'-object |
names<- | 'names<-' sets names in 'MSP'-object |
names<--method | 'names<-' sets names in 'MSP'-object |
NDP | Calculate the normalised dot product |
peaks | 'peaks' method for 'MSP'-class |
peaks-method | '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 |
show-method | '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 |
[ | Extract parts of a 'MSP'-object |
[-method | Extract parts of a 'MSP'-object |