rBiopaxParser: Parses BioPax files and represents them in R

Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.

AuthorFrank Kramer
Date of publicationNone
MaintainerFrank Kramer <dev@frankkramer.de>
LicenseGPL (>= 2)
Version2.14.0
https://github.com/frankkramer-lab/rBiopaxParser

View on Bioconductor

Man pages

addBiochemicalReaction: This function adds a new biochemical reaction to the biopax...

addBiopaxInstance: This function adds a new instance to an existing biopax...

addBiopaxInstances: This function adds new instances to an existing biopax model.

addControl: This function adds a new control to the biopax model.

addhash: Adds a hash in front of a string

addns: Add a namespace tag to the supplied classname string

addPathway: This function adds a new pathway to the biopax model.

addPathwayComponents: This function adds pathway components to an existing pathway

addPhysicalEntity: This function adds a new physical entity.

addPhysicalEntityParticipant: This function adds a new physical entity participant.

addPropertiesToBiopaxInstance: This function adds new properties to an existing biopax...

biopax: Biopax example data set

calcGraphOverlap: This function calculates the overlap of 2 graphs

checkValidity: This function checks the supplied biopax model for validity.

CLASS_INHERITANCE_BP2: CLASS_INHERITANCE_BP2

CLASS_INHERITANCE_BP3: CLASS_INHERITANCE_BP3

CLASS_PROPERTIES_BP2: CLASS_PROPERTIES_BP2

CLASS_PROPERTIES_BP3: CLASS_PROPERTIES_BP3

colorGraphNodes: This function colors the nodes of a graph.

combineNodes: This function gracefully combines nodes of a regulatory...

createBiopax: This function creates a new Biopax model from scratch

DATABASE_BIOPAX: DATABASE_BIOPAX

diffGraphs: This function returns the different nodes and edges between...

downloadBiopaxData: This function downloads Biopax data from online databases

generateNewUniqueID: This function generates a new unique id for a biopax model

getClassProperties: This function returns the properties of the supplied biopax...

getInstanceClass: This function returns the class name of the instance.

getInstanceProperty: This function returns all properties of the specified type...

getNeighborhood: This function returns the neighborhood of a physicalEntity

getParticipants: This function is used internally by pathway2Graph to obtain...

getReferencedIDs: This function returns a vector of ids of all instances...

getReferencingIDs: This function returns a vector of ids of all instances that...

getSubClasses: This function returns the subclasses of the supplied biopax...

getSuperClasses: This function returns the superclasses of the supplied biopax...

getXrefAnnotations: This function returns the annotations of the supplied...

hasProperty: Checks if instances in the biopax data.table have a given...

internal_checkArguments: This function checks the supplied arguments if they abid to...

internal_generateXMLfromBiopax: This function generates the xmlTree from the supplied biopax...

internal_getBiopaxModelAsDataFrame: This internal function parses the Biopax XML of the supplied...

internal_NrOfXMLNodes: This function is an internal function to count the Number of...

internal_propertyListToDF: Internal function to build a data.frame from the list of...

internal_resolvePhysicalEntityParticipant: This function resolves physicalEntityParticipantIDs to their...

internal_XMLInstance2DF: This function is an internal function that parses a Biopax...

intersectGraphs: This function returns a graph computed by the insection of...

isOfClass: Checks if instances in the biopax data.table are of the given...

isOfNamespace: Check if a classname is preceeded by a certain namespace tag...

isURL: Check if a string is an URL, preceeded by "http:"

layoutRegulatoryGraph: This function generates a (more or less) beautiful layout for...

listComplexComponents: This function lists all components of a given complex.

listInstances: Lists all instances that conform to the selection criteria.

listInteractionComponents: This function lists all components of a given interaction.

listPathwayComponents: This function lists all pathway components of a given...

listPathways: This function returns a list of all pathway ids.

mergePathways: This function merges two given pathways

pathway2AdjacancyMatrix: This function generates an adjacency matrix from the...

pathway2Geneset: This function generates the gene set of a pathway. This...

pathway2Graph: This function generates a directed graph from all the...

pathway2RegulatoryGraph: This function generates the regulatory graph from the...

plotRegulatoryGraph: This function layouts a regulatory graph and plots it using...

print.biopax: Print a biopax object.

rBiopaxParser-package: Parses BioPax level files and represents them in R

readBiopax: This function reads in a Biopax .owl file

removeDisconnectedParts: This function is used internally by pathway2Graph to remove...

removeInstance: This function removes an instance

removeNodes: This function gracefully removes nodes from a regulatory...

removeProperties: This function removes a property

selectInstances: Returns all instances that conform to the selection criteria.

splitComplex: This functions splits up a complex into its components.

striphash: Strips a hash in front of a string

stripns: Strips a namespace tag off a supplied classname string

transitiveClosure: This function generates the transitive closure of the...

transitiveReduction: This function generates the transitive reduction of the...

unfactorize: Replace factors/levels in a data.frame and use plain strings...

uniteGraphs: This function unites two graphs.

writeBiopax: This function writes out a biopax model.

Functions

addBiochemicalReaction Man page
addBiopaxInstance Man page
addBiopaxInstances Man page
addControl Man page
addhash Man page
addns Man page
addPathway Man page
addPathwayComponents Man page
addPhysicalEntity Man page
addPhysicalEntityParticipant Man page
addPropertiesToBiopaxInstance Man page
biopax Man page
biopaxexample Man page
biopaxLevel3Example Man page
calcGraphOverlap Man page
checkValidity Man page
CLASS_INHERITANCE_BP2 Man page
CLASS_INHERITANCE_BP3 Man page
CLASS_PROPERTIES_BP2 Man page
CLASS_PROPERTIES_BP3 Man page
colorGraphNodes Man page
combineNodes Man page
createBiopax Man page
DATABASE_BIOPAX Man page
diffGraphs Man page
downloadBiopaxData Man page
generateNewUniqueID Man page
getClassProperties Man page
getInstanceClass Man page
getInstanceProperty Man page
getNeighborhood Man page
getParticipants Man page
getReferencedIDs Man page
getReferencingIDs Man page
getSubClasses Man page
getSuperClasses Man page
getXrefAnnotations Man page
hasProperty Man page
internal_checkArguments Man page
internal_generateXMLfromBiopax Man page
internal_getBiopaxModelAsDataFrame Man page
internal_NrOfXMLNodes Man page
internal_propertyListToDF Man page
internal_resolvePhysicalEntityParticipant Man page
internal_XMLInstance2DF Man page
intersectGraphs Man page
isOfClass Man page
isOfNamespace Man page
isURL Man page
layoutRegulatoryGraph Man page
listComplexComponents Man page
listInstances Man page
listInteractionComponents Man page
listPathwayComponents Man page
listPathways Man page
mergePathways Man page
pathway2AdjacancyMatrix Man page
pathway2Geneset Man page
pathway2Graph Man page
pathway2RegulatoryGraph Man page
plotRegulatoryGraph Man page
print.biopax Man page
rBiopaxParser Man page
rBiopaxParser-package Man page
readBiopax Man page
removeDisconnectedParts Man page
removeInstance Man page
removeNodes Man page
removeProperties Man page
selectInstances Man page
splitComplex Man page
striphash Man page
stripns Man page
transitiveClosure Man page
transitiveReduction Man page
unfactorize Man page
uniteGraphs Man page
writeBiopax Man page

Files

rBiopaxParser/DESCRIPTION
rBiopaxParser/NAMESPACE
rBiopaxParser/NEWS
rBiopaxParser/R
rBiopaxParser/R/biopax2Classes.R rBiopaxParser/R/downloadBiopaxData.R rBiopaxParser/R/helperFunctions.R rBiopaxParser/R/modifyBiopax.R rBiopaxParser/R/parseBiopax.R rBiopaxParser/R/pathway2Graph.R rBiopaxParser/R/rBiopaxParser-package.R rBiopaxParser/R/selectBiopax.R rBiopaxParser/R/visualizeBiopax.R rBiopaxParser/R/writeBiopax.R
rBiopaxParser/README.md
rBiopaxParser/build
rBiopaxParser/build/vignette.rds
rBiopaxParser/data
rBiopaxParser/data/biopaxLevel3Example.RData
rBiopaxParser/data/biopaxexample.rda
rBiopaxParser/inst
rBiopaxParser/inst/CITATION
rBiopaxParser/inst/doc
rBiopaxParser/inst/doc/rBiopaxParserVignette.R
rBiopaxParser/inst/doc/rBiopaxParserVignette.Rnw
rBiopaxParser/inst/doc/rBiopaxParserVignette.pdf
rBiopaxParser/inst/unitTests
rBiopaxParser/inst/unitTests/test_biopax2Classes.R
rBiopaxParser/inst/unitTests/test_downloadBiopaxData.R
rBiopaxParser/inst/unitTests/test_helperFunctions.R
rBiopaxParser/man
rBiopaxParser/man/CLASS_INHERITANCE_BP2.Rd rBiopaxParser/man/CLASS_INHERITANCE_BP3.Rd rBiopaxParser/man/CLASS_PROPERTIES_BP2.Rd rBiopaxParser/man/CLASS_PROPERTIES_BP3.Rd rBiopaxParser/man/DATABASE_BIOPAX.Rd rBiopaxParser/man/addBiochemicalReaction.Rd rBiopaxParser/man/addBiopaxInstance.Rd rBiopaxParser/man/addBiopaxInstances.Rd rBiopaxParser/man/addControl.Rd rBiopaxParser/man/addPathway.Rd rBiopaxParser/man/addPathwayComponents.Rd rBiopaxParser/man/addPhysicalEntity.Rd rBiopaxParser/man/addPhysicalEntityParticipant.Rd rBiopaxParser/man/addPropertiesToBiopaxInstance.Rd rBiopaxParser/man/addhash.Rd rBiopaxParser/man/addns.Rd rBiopaxParser/man/biopax.Rd rBiopaxParser/man/calcGraphOverlap.Rd rBiopaxParser/man/checkValidity.Rd rBiopaxParser/man/colorGraphNodes.Rd rBiopaxParser/man/combineNodes.Rd rBiopaxParser/man/createBiopax.Rd rBiopaxParser/man/diffGraphs.Rd rBiopaxParser/man/downloadBiopaxData.Rd rBiopaxParser/man/generateNewUniqueID.Rd rBiopaxParser/man/getClassProperties.Rd rBiopaxParser/man/getInstanceClass.Rd rBiopaxParser/man/getInstanceProperty.Rd rBiopaxParser/man/getNeighborhood.Rd rBiopaxParser/man/getParticipants.Rd rBiopaxParser/man/getReferencedIDs.Rd rBiopaxParser/man/getReferencingIDs.Rd rBiopaxParser/man/getSubClasses.Rd rBiopaxParser/man/getSuperClasses.Rd rBiopaxParser/man/getXrefAnnotations.Rd rBiopaxParser/man/hasProperty.Rd rBiopaxParser/man/internal_NrOfXMLNodes.Rd rBiopaxParser/man/internal_XMLInstance2DF.Rd rBiopaxParser/man/internal_checkArguments.Rd rBiopaxParser/man/internal_generateXMLfromBiopax.Rd rBiopaxParser/man/internal_getBiopaxModelAsDataFrame.Rd rBiopaxParser/man/internal_propertyListToDF.Rd rBiopaxParser/man/internal_resolvePhysicalEntityParticipant.Rd rBiopaxParser/man/intersectGraphs.Rd rBiopaxParser/man/isOfClass.Rd rBiopaxParser/man/isOfNamespace.Rd rBiopaxParser/man/isURL.Rd rBiopaxParser/man/layoutRegulatoryGraph.Rd rBiopaxParser/man/listComplexComponents.Rd rBiopaxParser/man/listInstances.Rd rBiopaxParser/man/listInteractionComponents.Rd rBiopaxParser/man/listPathwayComponents.Rd rBiopaxParser/man/listPathways.Rd rBiopaxParser/man/mergePathways.Rd rBiopaxParser/man/pathway2AdjacancyMatrix.Rd rBiopaxParser/man/pathway2Geneset.Rd rBiopaxParser/man/pathway2Graph.Rd rBiopaxParser/man/pathway2RegulatoryGraph.Rd rBiopaxParser/man/plotRegulatoryGraph.Rd rBiopaxParser/man/print.biopax.Rd rBiopaxParser/man/rBiopaxParser-package.Rd rBiopaxParser/man/readBiopax.Rd rBiopaxParser/man/removeDisconnectedParts.Rd rBiopaxParser/man/removeInstance.Rd rBiopaxParser/man/removeNodes.Rd rBiopaxParser/man/removeProperties.Rd rBiopaxParser/man/selectInstances.Rd rBiopaxParser/man/splitComplex.Rd rBiopaxParser/man/striphash.Rd rBiopaxParser/man/stripns.Rd rBiopaxParser/man/transitiveClosure.Rd rBiopaxParser/man/transitiveReduction.Rd rBiopaxParser/man/unfactorize.Rd rBiopaxParser/man/uniteGraphs.Rd rBiopaxParser/man/writeBiopax.Rd
rBiopaxParser/tests
rBiopaxParser/tests/runTests.R
rBiopaxParser/vignettes
rBiopaxParser/vignettes/biopax2classgraph.pdf
rBiopaxParser/vignettes/biopaxsimple.pdf
rBiopaxParser/vignettes/mergedpw.pdf
rBiopaxParser/vignettes/newpathways2.png
rBiopaxParser/vignettes/rBiopaxParserVignette.Rnw
rBiopaxParser/vignettes/segclock.pdf
rBiopaxParser/vignettes/wntplot.pdf

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