MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
Version 1.2.0

MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data: create an MSP object, a format for MS/MS library data, bin m/z values of precursors, calculate similarity between precursors based on the normalised dot product 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.

Browse man pages Browse package API and functions Browse package files

AuthorThomas Naake <thomasnaake@googlemail.com> and Emmanuel Gaquerel <emmanuel.gaquerel@cos.uni-heidelberg.de>
Bioconductor views MassSpectrometry Metabolomics Visualization
Date of publicationNone
MaintainerThomas Naake <thomasnaake@googlemail.com>
LicenseGPL-2
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MetCirc")

Man pages

adduct: 'adduct' returns adduct ion names of compounds in...
adduct-set: 'adduct<-' sets adduct ion names in 'MSP'-object
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
classes: 'classes' returns class names of compounds in 'MSP'-object
classes-set: 'classes<-' sets information in 'MSP'-object
combine: 'combine' method for 'MSP'-class
compartmentTissue: Example data for 'MetCirc': 'compartmentTissue'
convert2MSP: Convert deconvoluted matrix into 'MSP'-object
convertExampleDF: Example data for 'MetCirc': convertExampleDF
convertMSP2MSP: Convert MSP data frame into object of 'MSP'-class
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 link matrix
cutUniquePrecursor: 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
getPrecursorMZ: 'getPrecursorMZ' returns precursor m/z values of an...
getRT: 'getRT' returns precursor RT values of an 'MSP'-object
highlight: Add links and highlight sectors
idMSMStoMSP-data: Example data for 'MetCirc': 'finalMSP'
information: 'information' returns information of metabolites in...
information-set: 'information<-' sets information in 'MSP'-object
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
msp2msp: Example data for 'MetCirc': 'msp2msp'
names: 'names' returns names in 'MSP'-object
names-set: 'names<-' sets names in 'MSP'-object
NDP: Calculate the normalised dot product
peaks: 'peaks' method for 'MSP'-class
plotCircos: Circular plot to visualise similarity
printInformationSelect: Display information on connected features of selected...
sd01_outputXCMS: Example data for 'MetCirc': 'sd01_outputXCMS'
sd02_deconvoluted: Example data for 'MetCirc': sd02_deconvoluted
shinyCircos: Interactive visualisation of similarity and navigation of...
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

MSP Man page
MSP-class Man page
NDP Man page Source code
[ Man page
[,MSP,numeric-method Man page
adduct Man page Source code
adduct,MSP-method Man page
adduct<- Man page
adduct<-,MSP,character-method Man page
allocatePrecursor2mz Man page Source code
binnedMSP Man page
binning Man page Source code
cart2Polar Man page Source code
circosLegend Man page Source code
classes Man page Source code
classes,MSP-method Man page
classes<- Man page
classes<-,MSP,character-method Man page
combine Man page
combine,MSP,MSP-method Man page
combine,MSP-method Man page
compartmentTissue Man page
convert2MSP Man page Source code
convertExampleDF Man page
convertMSP2MSP Man page Source code
createLink0Matrix Man page Source code
createLinkMatrix Man page Source code
createOrderedSimMat Man page Source code
createSimilarityMatrix Man page Source code
cutLinkMatrix Man page Source code
cutUniquePrecursor Man page Source code
finalMSP Man page
getBegEndIndMSP Man page Source code
getLinkMatrixIndices Man page Source code
getPrecursorMZ Man page Source code
getPrecursorMZ,MSP-method Man page
getRT Man page Source code
getRT,MSP-method Man page
highlight Man page Source code
idMSMStoMSP-data Man page
information Man page Source code
information,MSP-method Man page
information<- Man page
information<-,MSP,character-method Man page
length Man page
length,MSP-method Man page
minFragCart2Polar Man page Source code
msp2FunctionalLossesMSP Man page Source code
msp2msp Man page
names Man page
names,MSP-method Man page
names<- Man page
names<-,MSP,character-method Man page
peaks Man page
peaks,MSP-method Man page
plotCircos Man page Source code
printInformationSelect Man page Source code
sd01_outputXCMS Man page
sd02_deconvoluted Man page
shinyCircos Man page Source code
show Man page
show,MSP-method Man page
similarityMat Man page
thresholdLinkMatrix Man page Source code
tissue Man page
truncateName Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/NDP.R
R/allocatePrecursor2mz.R
R/binnedMSP-data.R
R/binning.R
R/convert2MSP.R
R/convertExampleDF-data.R
R/convertMSP2MSP-data.R
R/convertMSP2MSP.R
R/idMSMStissueproject-data.R
R/idMSMStoMSP-data.R
R/linkMatrix.R
R/plottingFunctions.R
R/sd01_outputXCMS-data.R
R/sd02_deconvoluted-data.R
R/shinyApp.R
R/similarityMat-data.R
build
build/vignette.rds
data
data/binnedMSP.RData
data/convertExampleDF.RData
data/convertMSP2MSP.RData
data/datalist
data/idMSMStissueproject.RData
data/idMSMStoMSP.RData
data/sd01_outputXCMS.RData
data/sd02_deconvoluted.RData
data/similarityMat.RData
inst
inst/NEWS
inst/doc
inst/doc/MetCirc.R
inst/doc/MetCirc.Rnw
inst/doc/MetCirc.pdf
inst/unitTests
inst/unitTests/test_NDP.R
inst/unitTests/test_allocatePrecursor2mz.R
inst/unitTests/test_binning.R
inst/unitTests/test_convert2MSP.R
inst/unitTests/test_convertMSP2MSP.R
inst/unitTests/test_linkMatrix.R
inst/unitTests/test_plottingFunctions.R
inst/unitTests/test_shinyApp.R
man
man/MSP.Rd
man/NDP.Rd
man/adduct-set.Rd
man/adduct.Rd
man/allocatePrecursor2mz.Rd
man/binnedMSP.Rd
man/binning.Rd
man/cart2Polar.Rd
man/circosLegend.Rd
man/classes-set.Rd
man/classes.Rd
man/combine.Rd
man/compartmentTissue.Rd
man/convert2MSP.Rd
man/convertExampleDF.Rd
man/convertMSP2MSP.Rd
man/createLink0Matrix.Rd
man/createLinkMatrix.Rd
man/createOrderedSimMat.Rd
man/createSimilarityMatrix.Rd
man/cutLinkMatrix.Rd
man/cutUniquePrecursor.Rd
man/extract-methods.Rd
man/getBegEndIndMSP.Rd
man/getLinkMatrixIndices.Rd
man/getPrecursorMZ.Rd
man/getRT.Rd
man/highlight.Rd
man/idMSMStoMSP-data.Rd
man/information-set.Rd
man/information.Rd
man/length-method.Rd
man/minFragCart2Polar.Rd
man/msp2FunctionalLossesMSP.Rd
man/msp2msp.Rd
man/names-set.Rd
man/names.Rd
man/peaks.Rd
man/plotCircos.Rd
man/printInformationSelect.Rd
man/sd01_outputXCMS.Rd
man/sd02_deconvoluted.Rd
man/shinyCircos.Rd
man/show-method.Rd
man/similarityMat.Rd
man/thresholdLinkMatrix.Rd
man/tissue.Rd
man/truncateName.Rd
tests
tests/runTests.R
vignettes
vignettes/Makefile
vignettes/MetCirc-blx.bib
vignettes/MetCirc-citations.bib
vignettes/MetCirc.Rnw
vignettes/MetCirc.run.xml
MetCirc documentation built on May 20, 2017, 10:22 p.m.