extractNonLinearSubpathways {CHRONOS} | R Documentation

## Non linear subpathway extraction from pathway graphs

### Description

Non linear subpathway extraction from pathway graphs

### Usage

    extractNonLinearSubpathways(graphs, pathways, a, b, k, filter, groupMode,
        export, 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.
`k` | Clique size.
`filter` | Filter the subpaths with user genes (TRUE).
`groupMode` | Expand paralogues ('expand') or collapse them to a single entry ('collapse').
`export` | Exports subpaths in CHRONOS/extdata/Output/Subpaths/Non-Linear/ <org> folder. Availiable formats are '.txt' and/or '.RData'.
`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)

To extract non linear subpaths from a pathway graph, all interactions between nodes of belonging to k-cliques are found. The ones that correspond

To extract non linear subpaths from a pathway graph, all interactions between nodes of belonging to k-cliques are found. The ones that correspond to actual interactions between genes make up the non linear subpath.

### Examples

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

    # Extract linear subpathways
    nliSubs  <- extractNonLinearSubpathways(graphs=graphs)

[Package CHRONOS version 1.12.0 Index]