dagFunctions: Utility functions to work with Directed Acyclic Graphs (DAG)

In llrs/topGO: Enrichment Analysis for Gene Ontology

Description

Basic functions to work witg DAGs

Usage

buildLevels(dag, root = NULL, leafs2root = TRUE)
getNoOfLevels(graphLevels)
getGraphRoot(dag, leafs2root = TRUE)
reverseArch(dirGraph, useAlgo = "sparse", useWeights = TRUE)

Arguments

dag	A graphNEL object.
root	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.

llrs/topGO documentation built on May 22, 2019, 12:16 p.m.