Man pages for PlantDefenseMetabolism/MetCirc
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
allocatePrecursor2mzallocatePrecursor2mz: Join two data sources
binnedMSPExample data for 'MetCirc': 'binnedMSP'
binningBin m/z values
cart2PolarCalculate polar coordinates from cartesian coordinates
circosLegendPlot 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
compartmentTissueExample data for 'MetCirc': 'compartmentTissue'
convert2MSPConvert deconvoluted matrix into 'MSP'-object
convertExampleDFExample data for 'MetCirc': convertExampleDF
convertMSP2MSPConvert MSP data frame into object of 'MSP'-class
createLink0MatrixCreate a link matrix
createLinkMatrixCreate a matrix which contains features to link (indices)
createOrderedSimMatUpdate colnames and rownames of a similarity matrix according...
createSimilarityMatrixCreate similarity matrix
cutLinkMatrixCreate a cut link matrix
cutUniquePrecursorGet unique precursor ions
extract-methodsExtract parts of a 'MSP'-object
getBegEndIndMSPGet beginning and end indices of each entry in a 'data.frame'...
getLinkMatrixIndicesGet indices in LinkMatrix of feature
getPrecursorMZ'getPrecursorMZ' returns precursor m/z values of an...
getRT'getRT' returns precursor RT values of an 'MSP'-object
highlightAdd links and highlight sectors
idMSMStoMSP-dataExample 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
minFragCart2PolarCalculate the nearest feature in polar coordinates given...
msp2FunctionalLossesMSPConvert MSP to MSP with functional losses
msp2mspExample data for 'MetCirc': 'msp2msp'
names'names' returns names in 'MSP'-object
names-set'names<-' sets names in 'MSP'-object
NDPCalculate the normalised dot product
peaks'peaks' method for 'MSP'-class
plotCircosCircular plot to visualise similarity
printInformationSelectDisplay information on connected features of selected...
sd01_outputXCMSExample data for 'MetCirc': 'sd01_outputXCMS'
sd02_deconvolutedExample data for 'MetCirc': sd02_deconvoluted
shinyCircosInteractive visualisation of similarity and navigation of...
show-method'show' method for 'MSP'-class
similarityMatExample data for 'MetCirc': 'similarityMat'
thresholdLinkMatrixThreshold a link matrix
tissueExample data for 'MetCirc': 'tissue'
truncateNameTruncate names
PlantDefenseMetabolism/MetCirc documentation built on May 8, 2019, 2:52 p.m.