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

Functions

[ Man page
allocatePrecursor2mz Man page
binnedMSP Man page
binning Man page
cart2Polar Man page
circosLegend Man page
combine Man page
combine,MSP-method Man page
combine,MSP,MSP-method Man page
compartmentTissue Man page
convert2MSP Man page
convertExampleDF Man page
createLink0Matrix Man page
createLinkMatrix Man page
createOrderedSimMat Man page
createSimilarityMatrix Man page
cutLinkMatrix Man page
cutUniquePreMZ Man page
finalMSP Man page
getBegEndIndMSP Man page
getLinkMatrixIndices Man page
getMetaboliteClass Man page
getMetaboliteClass,MSP-method Man page
getMetaboliteName Man page
getMetaboliteName,MSP-method Man page
getMSP Man page
getMSP,MSP-method Man page
getName Man page
getName,MSP-method Man page
getPrecursorMZ Man page
getPrecursorMZ,MSP-method Man page
getRT Man page
getRT,MSP-method Man page
highlight Man page
idMSMStoMSP-data Man page
length Man page
length,MSP-method Man page
minFragCart2Polar Man page
MSP Man page
msp2FunctionalLossesMSP Man page
MSP-class Man page
[,MSP,numeric,missing,missing-method Man page
NDP Man page
plotCircos Man page
printInformationHover Man page
sd01_outputXCMS Man page
sd02_deconvoluted Man page
setMetaboliteClass Man page
setMetaboliteClass,character,MSP-method Man page
setMetaboliteName Man page
setMetaboliteName,character,MSP-method Man page
setName Man page
setName,character,MSP-method Man page
shinyCircos Man page
show Man page
show,MSP-method Man page
similarityMat Man page
thresholdLinkMatrix Man page
tissue Man page
truncateName Man page

Files

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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