Man pages for PlantDefenseMetabolism/MetabolomicTools
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
| adduct | 'adduct' returns adduct ion names of compounds in... |
| adduct-set | '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-set | '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... |
| createSimilarityMatrix | Create similarity matrix |
| cutLinkMatrix | Create a cut link matrix |
| cutUniquePrecursor | Get unique precursor ions |
| extract-methods | Extract parts of a 'MSP'-object |
| getBegEndIndMSP | Get beginning and end indices of each entry in a 'data.frame'... |
| getLinkMatrixIndices | Get indices in LinkMatrix of feature |
| getPrecursorMZ | 'getPrecursorMZ' returns precursor m/z values of an... |
| 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... |
| information-set | 'information<-' sets information in 'MSP'-object |
| length-method | 'length' method for 'MSP'-class |
| minFragCart2Polar | Calculate the nearest feature in polar coordinates given... |
| MSP | MSP-class |
| msp2FunctionalLossesMSP | Convert MSP to MSP with functional losses |
| msp2msp | Example data for 'MetCirc': 'msp2msp' |
| names | 'names' returns names in 'MSP'-object |
| names-set | 'names<-' sets names in 'MSP'-object |
| NDP | Calculate the normalised dot product |
| peaks | 'peaks' method for 'MSP'-class |
| plotCircos | Circular plot to visualise similarity |
| printInformationSelect | Display information on connected features of selected... |
| sd01_outputXCMS | Example data for 'MetCirc': 'sd01_outputXCMS' |
| sd02_deconvoluted | Example data for 'MetCirc': sd02_deconvoluted |
| shinyCircos | Interactive visualisation of similarity and navigation of... |
| 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 |
