CHRONOS (version 1.0.3)

extractNonLinearSubpathways: 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/ 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 correspondTo 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)