subpathwayTypes: All subpathway types

In DEsubs: DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

Description

All subpathway types.

Usage

subpathwayTypes(grouping)

Arguments

grouping

By supplying one of the availiable groupings, specific subsets of availiable subpathway types can be extracted.

Details

Apart from the 124 distinct subpathway types, several groupings are availiable:

'all'

All subpathway options.

'all.bwd'

Forward propagation.

'all.fwd'

Backward propagation.

'all.stream'

All possible genes targeting or are targeted via a path starting from a gene of interest.

'all.neighbourhood'

All adjacent genes of a gene of interest with incoming or outgoing links.

'all.cascade'

A finite sequence of interactions connecting a sequence of genes starting or ending from a gene of interest.

'all.community'

Group of genes sharing common properties.

'all.component'

Subgraphs on which any two vertices are (strongly) connected to each other by paths.

'all.functional'

Forward and backward streams starting from genes/nodes with crucial functional role within the network. Individual options include GO_bp, GO_cc, GO_mf, KEGG, Disease_OMIM, Disease_GAD, Drug_DrugBank, miRNA, TF, DEG, which are defined below.

'all.GO_bp'

Genes acting as a bridge among Gene Ontology (GO) Biological Process terms.

'all.GO_cc'

Genes acting as a bridge among Gene Ontology (GO) Cellular Component terms.

'all.GO_mf'

Genes acting as a bridge among Gene Ontology (GO) Molecular Function terms.

'all.KEGG'

Genes acting as a bridge among KEGG pathway maps.

'all.Disease_OMIM'

Genes acting as a bridge among OMIM Disease targets.

'all.Disease_GAD'

Genes acting as a bridge among GAD Disease targets.

'all.Drug_DrugBank'

Genes acting as a bridge among DrugBank Drug targets.

'all.miRNA'

Genes acting as a bridge among microRNA-gene targets.

'all.TF'

Genes acting as a bridge among TF-gene targets.

'all.DEG'

Genes with highly Differentially expressed by each experimental data.

'all.topological'

Forward and backward streams starting from genes/nodes with crucial topological role within the network. Individual options include degree, betweenness, closeness, hub_score, eccentricity, page_rank, start_nodes which are defined below.

'all.degree'

Number of gene's adjacent interactions.

'all.betweenness'

Number of shortest paths from all vertices to others passing through a node.

'all.closeness'

Inverse of farness, which is the sum of distances to all other nodes.

'all.hub_score'

Kleinberg's hub centrality score.

'all.eccentricity'

Shortest path distance from the farthest other node in the graph.

'all.page_rank'

Google Page Rank.

'all.start_nodes'

Gene nodes without incoming links.

An exhaustive list of all 124 subpathway types follows:

STREAM-TOPOLOGICAL
'bwd.stream.topological.degree'	'fwd.stream.topological.degree'
'bwd.stream.topological.betweenness'	'fwd.stream.topological.betweenness'
'bwd.stream.topological.closeness'	'fwd.stream.topological.closeness'
'bwd.stream.topological.hub_score'	'fwd.stream.topological.hub_score'
'bwd.stream.topological.eccentricity'	'fwd.stream.topological.eccentricity'
'bwd.stream.topological.page_rank'	'fwd.stream.topological.page_rank'
'bwd.stream.topological.start_nodes'	'fwd.stream.topological.start_nodes'
STREAM-FUNCTIONAL
'bwd.stream.functional.GO_bp'	'fwd.stream.functional.GO_bp'
'bwd.stream.functional.GO_cc'	'fwd.stream.functional.GO_cc'
'bwd.stream.functional.GO_mf'	'fwd.stream.functional.GO_mf'
'bwd.stream.functional.KEGG'	'fwd.stream.functional.KEGG'
'bwd.stream.functional.Disease_OMIM'	'fwd.stream.functional.Disease_OMIM'
'bwd.stream.functional.Disease_GAD'	'fwd.stream.functional.Disease_GAD'
'bwd.stream.functional.Drug_DrugBank'	'fwd.stream.functional.Drug_DrugBank'
'bwd.stream.functional.miRNA'	'fwd.stream.functional.miRNA'
'bwd.stream.functional.TF'	'fwd.stream.functional.TF'
'bwd.stream.functional.DEG'	'fwd.stream.functional.DEG'
NEIGHBOURHOOD-TOPOLOGICAL
'bwd.neighbourhood.topological.degree'	'fwd.neighbourhood.topological.degree'
'bwd.neighbourhood.topological.betweenness'	'fwd.neighbourhood.topological.betweenness'
'bwd.neighbourhood.topological.closeness'	'fwd.neighbourhood.topological.closeness'
'bwd.neighbourhood.topological.hub_score'	'fwd.neighbourhood.topological.hub_score'
'bwd.neighbourhood.topological.eccentricity'	'fwd.neighbourhood.topological.eccentricity'
'bwd.neighbourhood.topological.page_rank'	'fwd.neighbourhood.topological.page_rank'
'bwd.neighbourhood.topological.start_nodes'	'fwd.neighbourhood.topological.start_nodes'
NEIGHBOURHOOD-FUNCTIONAL
'bwd.neighbourhood.functional.GO_bp'	'fwd.neighbourhood.functional.GO_bp'
'bwd.neighbourhood.functional.GO_cc'	'fwd.neighbourhood.functional.GO_cc'
'bwd.neighbourhood.functional.GO_mf'	'fwd.neighbourhood.functional.GO_mf'
'bwd.neighbourhood.functional.KEGG'	'fwd.neighbourhood.functional.KEGG'
'bwd.neighbourhood.functional.Disease_OMIM'	'fwd.neighbourhood.functional.Disease_OMIM'
'bwd.neighbourhood.functional.Disease_GAD'	'fwd.neighbourhood.functional.Disease_GAD'
'bwd.neighbourhood.functional.Drug_DrugBank'	'fwd.neighbourhood.functional.Drug_DrugBank'
'bwd.neighbourhood.functional.miRNA'	'fwd.neighbourhood.functional.miRNA'
'bwd.neighbourhood.functional.TF'	'fwd.neighbourhood.functional.DEG'
CASCADE-TOPOLOGICAL
'bwd.cascade.topological.degree'	'fwd.cascade.topological.degree'
'bwd.cascade.topological.betweenness'	'fwd.cascade.topological.betweenness'
'bwd.cascade.topological.closeness'	'fwd.cascade.topological.closeness'
'bwd.cascade.topological.hub_score'	'fwd.cascade.topological.hub_score'
'bwd.cascade.topological.eccentricity'	'fwd.cascade.topological.eccentricity'
'bwd.cascade.topological.page_rank'	'fwd.cascade.topological.page_rank'
'bwd.cascade.topological.start_nodes'	'fwd.cascade.topological.start_nodes'
CASCADE-FUNCTIONAL
'bwd.cascade.functional.GO_bp'	'fwd.cascade.functional.GO_bp'
'bwd.cascade.functional.GO_cc'	'fwd.cascade.functional.GO_cc'
'bwd.cascade.functional.GO_mf'	'fwd.cascade.functional.GO_mf'
'bwd.cascade.functional.KEGG'	'fwd.cascade.functional.KEGG'
'bwd.cascade.functional.Disease_OMIM'	'fwd.cascade.functional.Disease_OMIM'
'bwd.cascade.functional.Disease_GAD'	'fwd.cascade.functional.Disease_GAD'
'bwd.cascade.functional.Drug_DrugBank'	'fwd.cascade.functional.Drug_DrugBank'
'bwd.cascade.functional.miRNA'	'fwd.cascade.functional.miRNA'
'bwd.cascade.functional.TF'	'fwd.cascade.functional.TF'
'bwd.cascade.functional.DEG'	'fwd.cascade.functional.DEG'
COMMUNITY
'community.walktrap'	'community.edge_betweenness'
'community.fast_greedy'	'community.leading_eigen'
'community.infomap'	'community.louvain'
COMPONENT-CLIQUES
'component.max_cliques'	'component.decompose'
'component.3-cliques'	...
...	'component.9-cliques'
COMPONENT-CORENESS
'component.3-coreness'	...
...	'component.9-coreness'

Value

A vector of all 124 basic subpathway types. See Details section for handly groupings.

Examples

basic.types <- subpathwayTypes()
stream.types <- subpathwayTypes(grouping='all.stream')

DEsubs documentation built on Nov. 8, 2020, 8:31 p.m.