CHRONOS (version 1.0.3)

extractLinearSubpathways: Linear subpathway extraction from pathway graphs

Description

Linear subpathway extraction from pathway graphs

Usage

extractLinearSubpathways(graphs, pathways, a, b, filter, export, groupMode, verbose)

Arguments

graphs

Pathway graphs as returned from createPathwayGraphs.

pathways

The subset of pathways from whom subpathways are to be extracted. If missing, all pathway graphs are used.

a

Minimum subpathway length.

b

Maximum subpathway length.

filter

Filter the subpaths with user genes (TRUE).

export

Exports subpaths in CHRONOS/extdata/Output/Subpaths/Linear/ folder. Availiable formats are '.txt' and/or '.RData'.

groupMode

Expand paralogues ('expand') or collapse them to a single entry ('collapse').

verbose

Display informative messages (TRUE)

Requires previous execution of importExpressions.

Value

Returns a list consisting of

• A matrix of linear subpathways (subpaths)
• 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.

Examples

# Load pathway graphs from toy data
load(system.file('extdata', 'Examples//data.RData', package='CHRONOS'))

# Extract linear subpathways
linSubs <- extractLinearSubpathways(graphs=graphs)