MetCirc: A workflow to analyse and visualise metabolomics data

MetCirc comprises a workflow to interactively explore metabolomics data: create MSP, bin m/z values, calculate similarity between precursors and visualise similarities.

AuthorThomas Naake <thomasnaake@googlemail.com> and Emmanuel Gaquerel <emmanuel.gaquerel@cos.uni-heidelberg.de>
Date of publicationNone
MaintainerThomas Naake <thomasnaake@googlemail.com>
LicenseGPL-2
Version1.0.1

View on Bioconductor

Man 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

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...

createSimilarityMatrix: Create similarity matrix

cutLinkMatrix: Create a cut LinkMatrix

cutUniquePreMZ: Get unique precursor ions

extract-methods: Extract parts of a MSP object

getBegEndIndMSP: Get beginning and end indices of each entry in a data.frame...

getLinkMatrixIndices: Get indices in LinkMatrix of feature

getMetaboliteClass: getMetaboliteClass returns names of compounds in MSP object

getMetaboliteName: getMetaboliteName returns names of metabolites in MSP object

getMSP: getMSP method for MSP class

getName: getName returns names in MSP object

getPrecursorMZ: getPrecursorMZ returns precursor m/z values of an MSP object

getRT: getRT returns precursor RT values of an MSP object

highlight: Add links and highlight sectors

idMSMStoMSP-data: Example data for 'MetCirc': 'finalMSP'

length-method: length method for MSP class

minFragCart2Polar: Calculate the nearest feature in polar coordinates given...

MSP: 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...

setMetaboliteName: setMetaboliteName sets metabolite names in MSP objects

setName: setName sets names in MSP objects

shinyCircos: Interactive visualisation of similar precursors

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

Files in this package

MetCirc/DESCRIPTION
MetCirc/NAMESPACE
MetCirc/R
MetCirc/R/NDP.R MetCirc/R/allocatePrecursor2mz.R MetCirc/R/binnedMSP-data.R MetCirc/R/binning.R MetCirc/R/convert2MSP.R MetCirc/R/convertExampleDF-data.R MetCirc/R/idMSMStissueproject-data.R MetCirc/R/idMSMStoMSP-data.R MetCirc/R/linkMatrix.R MetCirc/R/plottingFunctions.R MetCirc/R/sd01_outputXCMS-data.R MetCirc/R/sd02_deconvoluted-data.R MetCirc/R/shinyApp.R MetCirc/R/similarityMat-data.R
MetCirc/Readme.md
MetCirc/build
MetCirc/build/vignette.rds
MetCirc/data
MetCirc/data/binnedMSP.RData
MetCirc/data/convertExampleDF.RData
MetCirc/data/datalist
MetCirc/data/idMSMStissueproject.RData
MetCirc/data/idMSMStoMSP.RData
MetCirc/data/sd01_outputXCMS.RData
MetCirc/data/sd02_deconvoluted.RData
MetCirc/data/similarityMat.RData
MetCirc/inst
MetCirc/inst/NEWS
MetCirc/inst/doc
MetCirc/inst/doc/MetCirc.R
MetCirc/inst/doc/MetCirc.Rnw
MetCirc/inst/doc/MetCirc.pdf
MetCirc/inst/unitTests
MetCirc/inst/unitTests/test_NDP.R
MetCirc/inst/unitTests/test_allocatePrecursor2mz.R
MetCirc/inst/unitTests/test_binning.R
MetCirc/inst/unitTests/test_convert2MSP.R
MetCirc/inst/unitTests/test_linkMatrix.R
MetCirc/inst/unitTests/test_plottingFunctions.R
MetCirc/inst/unitTests/test_shinyApp.R
MetCirc/man
MetCirc/man/MSP.Rd MetCirc/man/NDP.Rd MetCirc/man/allocatePrecursor2mz.Rd MetCirc/man/binnedMSP.Rd MetCirc/man/binning.Rd MetCirc/man/cart2Polar.Rd MetCirc/man/circosLegend.Rd MetCirc/man/combine.Rd MetCirc/man/compartmentTissue.Rd MetCirc/man/convert2MSP.Rd MetCirc/man/convertExampleDF.Rd MetCirc/man/createLink0Matrix.Rd MetCirc/man/createLinkMatrix.Rd MetCirc/man/createOrderedSimMat.Rd MetCirc/man/createSimilarityMatrix.Rd MetCirc/man/cutLinkMatrix.Rd MetCirc/man/cutUniquePreMZ.Rd MetCirc/man/extract-methods.Rd MetCirc/man/getBegEndIndMSP.Rd MetCirc/man/getLinkMatrixIndices.Rd MetCirc/man/getMSP.Rd MetCirc/man/getMetaboliteClass.Rd MetCirc/man/getMetaboliteName.Rd MetCirc/man/getName.Rd MetCirc/man/getPrecursorMZ.Rd MetCirc/man/getRT.Rd MetCirc/man/highlight.Rd MetCirc/man/idMSMStoMSP-data.Rd MetCirc/man/length-method.Rd MetCirc/man/minFragCart2Polar.Rd MetCirc/man/msp2FunctionalLossesMSP.Rd MetCirc/man/plotCircos.Rd MetCirc/man/printInformationHover.Rd MetCirc/man/sd01_outputXCMS.Rd MetCirc/man/sd02_deconvoluted.Rd MetCirc/man/setMetaboliteClass.Rd MetCirc/man/setMetaboliteName.Rd MetCirc/man/setName.Rd MetCirc/man/shinyCircos.Rd MetCirc/man/show-method.Rd MetCirc/man/similarityMat.Rd MetCirc/man/thresholdLinkMatrix.Rd MetCirc/man/tissue.Rd MetCirc/man/truncateName.Rd
MetCirc/tests
MetCirc/tests/runTests.R
MetCirc/vignettes
MetCirc/vignettes/Makefile
MetCirc/vignettes/MetCirc-blx.bib
MetCirc/vignettes/MetCirc-citations.bib
MetCirc/vignettes/MetCirc.Rnw
MetCirc/vignettes/MetCirc.run.xml

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