A character vector specifing the root(s) of the DAG. If
not specified the root node is autmatically computed.
leafs2root
The leafs2root parameter tell if the graph has edges
directed from the leaves to the root, or vice-versa
graphLevels
An object of type list, returned by the buildLevels function.
dirGraph
A graphNEL object containing a directed graph.
useAlgo
A character string specifing one of the following options
c("sparse", "normal"). By default, useAlgo = "sparse", a sparce matrix object is
used to transpose the adjacency matrix. Otherwise a standard R
martix is used.
useWeights
If weights should be used (if useAlgo =
"normal" then the weigths are used anyway)
Details
buildLevels function determines the levels of a Directed
Acyclic Graph (DAG). The level of a node is defined as the longest
path from the node to the root. The function take constructs a named
list containg varios information about each nodes level. The root has
level 1.
getNoOfLevels - a convenient function to extract the number of
levels from the object returned by buildLevels
getGraphRoot finds the root(s) of the DAG
reverseArch - simple function to invert the direction of edges
in a DAG. The returned graph is of class graphNEL. It can use either
simple matrices or sparse matrices (SparseM library)
Value
buildLevels returns a list containing:
level2nodes
Environment where the key is the level number
with the value being the nodes on that level.
nodes2level
Environment where the key is the node label (the GO
ID) and the value is the level on which that node lies.
noOfLevels
The number of levels
noOfNodes
The number of nodes
An object of class graphNEL-class is returned.
Author(s)
Adrian Alexa
See Also
topGOdata-class,
inducedGraph
Examples
##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.