Parses BioPax files and represents them in R

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Documentation for package ‘rBiopaxParser’ version 2.44.0

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rBiopaxParser-package Parses BioPax level files and represents them in R
addBiochemicalReaction This function adds a new biochemical reaction to the biopax model.
addBiopaxInstance This function adds a new instance to an existing biopax model.
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 instance.
biopax Biopax example data set
biopaxexample Biopax example data set
biopaxLevel3Example 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 graph.
createBiopax This function creates a new Biopax model from scratch
DATABASE_BIOPAX DATABASE_BIOPAX
diffGraphs This function returns the different nodes and edges between graph1 and graph2.
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 class.
getInstanceClass This function returns the class name of the instance.
getInstanceProperty This function returns all properties of the specified type for an instance.
getNeighborhood This function returns the neighborhood of a physicalEntity
getParticipants This function is used internally by pathway2Graph to obtain physical entities participating in an interaction.
getReferencedIDs This function returns a vector of ids of all instances referenced by the specified instance.
getReferencingIDs This function returns a vector of ids of all instances that reference the supplied id.
getSubClasses This function returns the subclasses of the supplied biopax class.
getSuperClasses This function returns the superclasses of the supplied biopax class.
getXrefAnnotations This function returns the annotations of the supplied instances.
hasProperty Checks if instances in the biopax data.table have a given property
internal_checkArguments This function checks the supplied arguments if they abid to the given restrictions
internal_generateXMLfromBiopax This function generates the xmlTree from the supplied biopax model.
internal_getBiopaxModelAsDataFrame This internal function parses the Biopax XML of the supplied biopax model and returns it in the data.frame format.
internal_NrOfXMLNodes This function is an internal function to count the Number of nodes and child nodes of an XMLNode.
internal_propertyListToDF Internal function to build a data.frame from the list of properties for a new instance
internal_resolvePhysicalEntityParticipant This function resolves physicalEntityParticipantIDs to their corresponding physicalEntityIDs
internal_XMLInstance2DF This function is an internal function that parses a Biopax XMLNode.
intersectGraphs This function returns a graph computed by the insection of supplied graph1 and graph2.
isOfClass Checks if instances in the biopax data.table are of the given class
isOfNamespace Check if a classname is preceeded by a certain namespace tag like in "namespace:classname"
isURL Check if a string is an URL, preceeded by "http:"
layoutRegulatoryGraph This function generates a (more or less) beautiful layout for a regulatory graph.
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 pathway.
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 activations/inhibitions of a pathway in a biopax model. This function internally first calls pathway2RegulatoryGraph, then converts the regulatory graph to an adjacency matrix. See pathway2RegulatoryGraph for more details.
pathway2Geneset This function generates the gene set of a pathway. This function generates a gene set of all physicalEntity's of a pathway. First all interactions of the pathway are retrieved and all components of these interactions are then listed.
pathway2Graph This function generates a directed graph from all the interactions of a specified pathway in a biopax model. Edges with no direction are indicated by a 0 weight.
pathway2RegulatoryGraph This function generates the regulatory graph from the activations/inhibitions of a pathway in a biopax model. This functions builds a graph from the pathway components of the supplied pathway. Only instances of class 'control' are considered, this leads a functinal graph with all edges either representing activations or inhibitions. No transports, no translocation, etc. If desired complexes can be split up into several nodes, this can sometimes lead to a more complex and cluttered graph. There can not be multiple edges between 2 nodes. Whenever duplicated edges are generated (especially by splitting up complexes) a warning is thrown.
plotRegulatoryGraph This function layouts a regulatory graph and plots it using Rgraphviz.
print.biopax Print a biopax object.
rBiopaxParser 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 the smaller disconnected parts of the pathway graph.
removeInstance This function removes an instance
removeNodes This function gracefully removes nodes from a regulatory graph.
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 supplied graph.
transitiveReduction This function generates the transitive reduction of the supplied graph.
unfactorize Replace factors/levels in a data.frame and use plain strings instead
uniteGraphs This function unites two graphs.
writeBiopax This function writes out a biopax model.