Package: MetCirc 1.37.0

Thomas Naake

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

MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data. MetCirc uses the Spectra object infrastructure defined in the package Spectra that stores MS/MS spectra. MetCirc offers functionality to calculate similarity between precursors based on the normalised dot product, neutral losses or user-defined functions and visualise similarities in a circular layout. Within the interactive framework the user can annotate MS/MS features based on their similarity to (known) related MS/MS features.

Authors:Thomas Naake <[email protected]>, Johannes Rainer <[email protected]> and Emmanuel Gaquerel <[email protected]>

MetCirc_1.37.0.tar.gz
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MetCirc.pdf |MetCirc.html✨
MetCirc/json (API)
NEWS

# Install 'MetCirc' in R:
install.packages('MetCirc', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:MetCirc-1.37.0(bioc 3.21)MetCirc-1.36.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

shinyappsmetabolomicsmassspectrometryvisualization

3.48 score 2 scripts 244 downloads 3 mentions 15 exports 74 dependencies

Last updated 2 months agofrom:9687bdfb3f. Checks:ERROR: 3 WARNING: 4. Indexed: yes.

TargetResultDate
Doc / VignettesFAILDec 09 2024
R-4.5-winWARNINGDec 09 2024
R-4.5-linuxWARNINGDec 09 2024
R-4.4-winWARNINGDec 09 2024
R-4.4-macWARNINGDec 09 2024
R-4.3-winERRORSep 30 2024
R-4.3-macERRORSep 30 2024

Exports:cart2PolarcircosLegendconvertMsp2SpectracreateLink0dfcreateLinkDfcutLinkDfgetLinkDfIndiceshighlightminFragCart2PolarneutrallossorderSimilarityMatrixplotCircosplotSpectrashinyCircosthresholdLinkDf

Dependencies:amapbase64encBHBiocGenericsBiocParallelbslibcachemcirclizecliclueclustercodetoolscolorspacecommonmarkcpp11crayondigestfansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsggplot2GlobalOptionsgluegtablehtmltoolshttpuvIRangesisobandjquerylibjsonlitelabelinglambda.rlaterlatticelifecyclemagrittrMASSMatrixmemoiseMetaboCoreUtilsmgcvmimeMsCoreUtilsmunsellnlmepillarpkgconfigpromisesProtGenericsR6rappdirsRColorBrewerRcpprlangS4VectorssassscalesshapeshinysnowsourcetoolsSpectratibbleutf8vctrsviridisLitewithrxtable

Readme and manuals

Help Manual

Help pageTopics
Calculate polar coordinates from cartesian coordinatescart2Polar
Plot a legend for circos plotcircosLegend
Example data for `MetCirc`: `compartmentTissue`compartmentTissue
Example data for `MetCirc`: convertExampleDFconvertExampleDF
Convert MSP data frame into object of class 'Spectra'convertMsp2Spectra
Create a link matrixcreateLink0df
Create a data frame which contains features to link (indices)createLinkDf
Create a cut data frame with information on linkscutLinkDf
Get indices in 'linkDf' of featuregetLinkDfIndices
Add links and highlight sectorshighlight
Calculate the nearest feature in polar coordinates given cartesian coordinatesminFragCart2Polar
Example data for `MetCirc`: `msp2spectra`msp2spectra
Calculate similarity based on neutral lossesneutralloss
Order columns and rows of a similarity matrix according to m/z, retention time and clusteringorderSimilarityMatrix
Circular plot to visualize similarityplotCircos
Plot pair-wise spectraplotSpectra
Display information on connected features of selected featuresprintInformationSelect
Record a plot of filled features and the degree of featuresrecordPlotFill_degreeFeatures
Return a 'recordedplot' of 'plotCircos' plot with 'highlight = TRUE'recordPlotHighlight
Plot plotCircos or highlightreplayPlotAdd
Wrapper for 'replayPlot'replayPlotOrder
Example data for `MetCirc`: `sd01_outputXCMS`sd01_outputXCMS
Example data for `MetCirc`: sd02_deconvolutedsd02_deconvoluted
Select variable based on conditionselect
Interactive visualisation of similarity and navigation of MS/MS featuresshinyCircos
Example data for `MetCirc`: `similarityMat`similarityMat
Get MS/MS spectra that are present in conditionspectraCondition
Example data for `MetCirc`: `sps_tissue`sps_tissue
Threshold a data frame containing information on linksthresholdLinkDf
Example data for `MetCirc`: `tissue`tissue
Get typeMatch and link0 data frametypeMatch_link0