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| 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 |
| combine-method | 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 |
| finalMSP | Example data for 'MetCirc': 'finalMSP' |
| getBegEndIndMSP | Get beginning and end indices of each entry in a data.frame in msp format |
| getLinkMatrixIndices | Get indices in LinkMatrix of feature |
| getMetaboliteClass | getMetaboliteClass returns names of compounds in MSP object |
| getMetaboliteClass-method | getMetaboliteClass returns names of compounds in MSP object |
| getMetaboliteName | getMetaboliteName returns names of metabolites in MSP object |
| getMetaboliteName-method | getMetaboliteName returns names of metabolites in MSP object |
| getMSP | getMSP method for MSP class |
| getMSP-method | getMSP method for MSP class |
| getName | getName returns names in MSP object |
| getName-method | getName returns names in MSP object |
| 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' |
| 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 |
| NDP | Calculate the normalised dot product |
| 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 |
| setMetaboliteClass-method | setMetaboliteClass sets class names of compounds in MSP objects |
| setMetaboliteName | setMetaboliteName sets metabolite names in MSP objects |
| setMetaboliteName-method | setMetaboliteName sets metabolite names in MSP objects |
| setName | setName sets names in MSP objects |
| setName-method | setName sets names in MSP objects |
| shinyCircos | Interactive visualisation of similar precursors |
| 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 |