A list of processed pathway graphs adjacency matrices (adjMats)
A list of processed pathway genes and interactions between them
(lexicon)
Details
Subpath filtering supports the removal of subpaths that have at least
one member not belonging to the set of user supplied genes. These genes
are extracted from the user's mRNA expressions matrix.Thus, the execution
of importExpressions is a prerequisite.
To extract linear subpathways from a pathway graph, all possible start
and end nodes are considered. A start node has only outgoing edges while
an end node only has incoming edges. For each such pair, all linear
subpathways are found by traversing the corresponding graph. Since the
initial pathway graph's nodes contain one or more genes, resulting
subpathways consist of bins of one or more genes. These subpaths are
expanded to subpathways with one gene per bin in order to obtain usable
subpathways.
# Load pathway graphs from toy dataload(system.file('extdata', 'Examples//data.RData', package='CHRONOS'))
# Extract linear subpathwayslinSubs <- extractLinearSubpathways(graphs=graphs)