A workflow to analyse and visualise metabolomics data


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Documentation for package ‘MetCirc’ version 1.0.1

Help Pages

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