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 |
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 |
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" |
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. |
pathway2Geneset | This function generates the gene set of a pathway. |
pathway2RegulatoryGraph | This function generates the regulatory graph from the activations/inhibitions of a pathway in a biopax model. |
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 |
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. |