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 |