pathway2Geneset
(Package: rBiopaxParser) :
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.
● Data Source:
BioConductor
● Keywords:
● Alias: pathway2Geneset
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pathway2RegulatoryGraph
(Package: rBiopaxParser) :
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.
● Data Source:
BioConductor
● Keywords:
● Alias: pathway2RegulatoryGraph
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plotRegulatoryGraph
(Package: rBiopaxParser) :
This function layouts a regulatory graph and plots it using Rgraphviz.
This function takes a regulatory graph as generated by pathway2regulatoryGraph and plots it using standard layout options of layoutRegulatoryGraph. This function is a wrapper for layoutRegulatoryGraph with standard parameters. Subgraphs can be painted with different colors. This can be done by passing parameter subgraph a list of character vectors with node names.
● Data Source:
BioConductor
● Keywords:
● Alias: plotRegulatoryGraph
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Print a biopax object.
● Data Source:
BioConductor
● Keywords:
● Alias: print.biopax
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Parses BioPax files and represents them in R
● Data Source:
BioConductor
● Keywords: package
● Alias: rBiopaxParser, rBiopaxParser-package
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readBiopax
(Package: rBiopaxParser) :
This function reads in a Biopax .owl file
This function reads in a Biopax .owl file and generates the internal data.frame format used in this package. This function can take a while with really big Biopax files like NCIs Pathway Interaction Database or Reactome. In almost every case this is your starting point. Returns a biopax model, which is a list with named elements:
● Data Source:
BioConductor
● Keywords:
● Alias: readBiopax
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This function removes an instance from an existing biopax model.
● Data Source:
BioConductor
● Keywords:
● Alias: removeInstance
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removeNodes
(Package: rBiopaxParser) :
This function gracefully removes nodes from a regulatory graph.
This function gracefully removes nodes from a regulatory graph. If the node to be removed has both parent and child nodes, these are connected directly. The weight of the new direct edge is the product of multiplying the incomming and outgoing edge weights of the original node.
● Data Source:
BioConductor
● Keywords:
● Alias: removeNodes
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This function removes a property fram an existing biopax instance.
● Data Source:
BioConductor
● Keywords:
● Alias: removeProperties
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selectInstances
(Package: rBiopaxParser) :
Returns all instances that conform to the selection criteria.
Returns all instances that conform to the selection criteria. This function returns a subset of the internal data.table of the biopax object. Selection criteria are wether instances belong to a certain class or have the specified id, property or name. Setting a criteria to NULL ignores this criteria. If returnValues is set to FALSE only the selector (a logical vector with length of the internal data.table) is returned, otherwise the selected data is returned. If includeSubClasses is set to TRUE the class criteria is broadened to include all classes that inherit from the given class, e.g. if class="control" and includeSubClasses=TRUE the function will select catalyses and modulations too, since they are a subclass of class control. If includeReferencedInstances is set to TRUE all instances that are being referenced by the selected instances are being selected too. The parameter works recursively, this means for example that a selected pathway and all it's interactions, complexes, molecules and annotations are returned if this parameter is set to true. This parameter is especially helpful if you want to migrate or merge knowledge from different data bases.
● Data Source:
BioConductor
● Keywords:
● Alias: selectInstances
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