| gpml-utility {WayFindR} | R Documentation |
Utility Functions to Parse GPML FIles
Description
Extract entities of different types from GPML files in order to convert the pathway to a mathematical graph that we can compute on.
Usage
collectEdges(xmldoc)
collectNodes(xmldoc)
collectGroups(xmldoc, allnodes)
collectAnchors(xmldoc)
collectLabels(xmldoc)
collectShapes(xmldoc)
Arguments
xmldoc |
Either the name of an XML file meeting the
specifications of the Genomic Pathway Markup Language (GPML), or an
object of class |
allnodes |
A data frame containing node information, in the format
produced by the |
Details
These functions are primarily intended as utility functions that
implement processes required by the main function in the package,
GPMLtoIgraph. They have been made accessible to
the end user for use in debugging problematic GPML files or to reuse
the GPML files in contexts other than the one we focus on in this
package.
While the meaning of nodes (known as DataNodes in GPML) and
edges (known as Interactions in GPML) should be obvious, some
of the other objects are less so. For example, an Anchor in
GPML is an invisible object used to allow an edge to point to
another edge instead of to a node. That structure isn't allowed in
graphs in mathematics or computer science. WayFindR handles
this by creating a new node type to represent the anchor position,
breaking the target edge into two pieces separated by the anchor, and
adding an edge from the source of the anchored edge to the new node.
In GPML, a Label is a text box allowing extra information to be
placed on a pathway, and a Shape is a graphical display object. The
definition type document (DTD) for GPML describes both of these
entities as non-semantic, intending them for display purposes
only. However, some authors of pathways in the WikiPathways database
use such objects as the (usually, final or "leaf") targets of
interaction edges. When that happens, the WayFindR package
deals with it by creating actual nodes to represent such labels or
shapes. Other labels and shapes are ignored.
GPML also uses the idea of a Group as a first class object in
their DTD. These are defined as "A collection of structurally or
functionally similar or related pathway elements." The GPML file
subclassifies some groups as "Complexes", indicating that they
represent physical interactions and bindings between two or more
molecules. Other groups may simply indicate that there is a related set
of molecules (for example, STAT2 and STA3) that play the same role at
this point in the pathway. WayFindR deals with groups by
creating a new node to represent the group as a whole and expanding
the component genes into nodes with a single "contained" edge that
points to the new group node.
Value
The collectEdges function returns a data frame with three
columns (Source, Target, and MIM), where each row
describes one edge (or "Interaction" in the GPML terminology) of the
pathway/graph. The Source and Target columns are the
alphanumeric identifiers of items decribing nodes. The MIM
column is the edge type in GPML, which often contains terminology based
on the "Molecular Interaction Map" standard. When creating an
igraph object from a pathway, the first two columns are
used as identifiers to define the nodes at each end of the edge.
The collectNodes function returns a data frame with three
columns (GraphId, label, and Type), where each row describes node
or vertex of the pathway/graph. The GraphId column is a unique
alphanumeric identifier. The label column is a human-readable
name for the node, often the official gene symbol. When creating an
igraph object from a pathway, the first column is used as
identifier to define the node. Also, the plot method for
igraphs recognizes the term label as a column that
defines the text that should be displayed in a node.
The collectAnchors function returns a list containing a
nodes element (in the same format returned by
collectNodes) and an edges element (in the same format
returned by collectEdges). The collectGroups function
returns a list with nodes and edges components, just
like the one from collectAnchors.
Both the collectLabels and collectShapes functions return
the same kind of data frame that is returned by collectNodes.
Author(s)
Kevin R. Coombes krc@silicovore.com, Polina Bombina pbombina@augusta.edu
Examples
xmlfile <- system.file("pathways/WP3850.gpml", package = "WayFindR")
xmldoc <- XML::xmlParseDoc(xmlfile)
edges <- collectEdges(xmldoc)
nodes <- collectNodes(xmldoc)
anchors <- collectAnchors(xmldoc)
labels <- collectLabels(xmldoc)
edges <- collectShapes(xmldoc)
groups <- collectGroups(xmldoc, nodes)