# Parses BioPax files and represents them in R

## Documentation for package ‘rBiopaxParser’ version 2.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.