extractNonLinearSubpathways: Non linear subpathway extraction from pathway graphs

In CHRONOS: CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

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)

CHRONOS documentation built on Nov. 8, 2020, 8:30 p.m.