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

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Documentation for package ‘MetCirc’ version 1.38.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

cart2Polar	Calculate polar coordinates from cartesian coordinates
circosLegend	Plot a legend for circos plot
compartmentTissue	Example data for 'MetCirc': 'compartmentTissue'
convertExampleDF	Example data for 'MetCirc': convertExampleDF
convertMsp2Spectra	Convert MSP data frame into object of class 'Spectra'
createLink0df	Create a link matrix
createLinkDf	Create a data frame which contains features to link (indices)
cutLinkDf	Create a cut data frame with information on links
getLinkDfIndices	Get indices in 'linkDf' of feature
highlight	Add links and highlight sectors
minFragCart2Polar	Calculate the nearest feature in polar coordinates given cartesian coordinates
msp2spectra	Example data for 'MetCirc': 'msp2spectra'
neutralloss	Calculate similarity based on neutral losses
orderSimilarityMatrix	Order columns and rows of a similarity matrix according to m/z, retention time and clustering
plotCircos	Circular plot to visualize similarity
plotSpectra	Plot pair-wise spectra
printInformationSelect	Display information on connected features of selected features
recordPlotFill_degreeFeatures	Record a plot of filled features and the degree of features
recordPlotHighlight	Return a 'recordedplot' of 'plotCircos' plot with 'highlight = TRUE'
replayPlotAdd	Plot plotCircos or highlight
replayPlotOrder	Wrapper for 'replayPlot'
sd01_outputXCMS	Example data for 'MetCirc': 'sd01_outputXCMS'
sd02_deconvoluted	Example data for 'MetCirc': sd02_deconvoluted
select	Select variable based on condition
shinyCircos	Interactive visualisation of similarity and navigation of MS/MS features
similarityMat	Example data for 'MetCirc': 'similarityMat'
spectraCondition	Get MS/MS spectra that are present in condition
sps_tissue	Example data for 'MetCirc': 'sps_tissue'
thresholdLinkDf	Threshold a data frame containing information on links
tissue	Example data for 'MetCirc': 'tissue'
typeMatch_link0	Get typeMatch and link0 data frame