MetCirc: MetCirc - a workflow to analyse and visualise metabolomics data

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

Author
Thomas Naake <naake@stud.uni-heidelberg.de> and Emmanuel Gaquerel <emmanuel.gaquerel@cos.uni-heidelberg.de>
Date of publication
None
Maintainer
Thomas Naake <naake@stud.uni-heidelberg.de>
License
GPL-2
Version
1.0.0

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