Navigating mass spectral similarity in high-resolution MS/MS metabolomics data


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Documentation for package ‘MetCirc’ version 1.10.0

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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