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+

+

+\name{subpathwayTypes}

+\alias{subpathwayTypes}

+\title{All subpathway types}

+\usage{

+subpathwayTypes(grouping)

+}

+\arguments{

+\item{grouping}{By supplying one of the availiable groupings, specific 

+subsets of availiable subpathway types can be extracted.}

+}

+\value{

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

+groupings.

+}

+\description{

+All subpathway types.

+}

+\details{

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

+\describe{

+\item{'all'}{ All subpathway options. }

+\item{'all.bwd'}{ Forward propagation. }

+\item{'all.fwd'}{Backward propagation. }

+\item{'all.stream'}{All possible genes targeting or are targeted 

+via a path starting from a gene of interest.}

+\item{'all.neighbourhood'}{All adjacent genes of a gene of interest with 

+incoming or outgoing links.}

+\item{'all.cascade'}{A finite sequence of interactions connecting a sequence 

+of genes starting or ending from a gene of interest.}

+\item{'all.community'}{Group of genes sharing common properties.}

+\item{'all.component'}{Subgraphs on which any two vertices are (strongly)

+connected to each other by paths.}

+\item{ }{}

+\item{'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.}

+\item{'all.GO_bp'}{Genes acting as a bridge among Gene Ontology (GO) 

+Biological Process terms. }

+\item{'all.GO_cc'}{Genes acting as a bridge among Gene Ontology (GO) 

+Cellular Component terms. }

+\item{'all.GO_mf'}{Genes acting as a bridge among Gene Ontology (GO) 

+Molecular Function terms. }

+\item{'all.KEGG'}{Genes acting as a bridge among KEGG pathway maps. }

+\item{'all.Disease_OMIM'}{Genes acting as a bridge among OMIM Disease 

+targets.}

+\item{'all.Disease_GAD'}{Genes acting as a bridge among GAD Disease targets.}

+\item{'all.Drug_DrugBank'}{Genes acting as a bridge among DrugBank Drug 

+targets.}

+\item{'all.miRNA'}{Genes acting as a bridge among microRNA-gene targets. }

+\item{'all.TF'}{Genes acting as a bridge among TF-gene targets. }

+\item{'all.DEG'}{Genes with highly Differentially expressed by each 

+experimental data. }

+\item{}{}

+\item{'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.}

+\item{'all.degree'}{Number of gene's adjacent interactions.}

+\item{'all.betweenness'}{Number of shortest paths from all vertices to  

+others passing through a node.}

+\item{'all.closeness'}{Inverse of farness, which is the sum of distances 

+to all other nodes.}

+\item{'all.hub_score'}{Kleinberg's hub centrality score.}

+\item{'all.eccentricity'}{Shortest path distance from the farthest other 

+node in the graph.}

+\item{'all.page_rank'}{Google Page Rank.}

+\item{'all.start_nodes'}{Gene nodes without incoming links.}

+\item{}{}

+}

+

+An exhaustive list of all 124 subpathway types follows:

+

+\tabular{ll}{

+    \tab  \cr

+    STREAM-TOPOLOGICAL  \tab  \cr

+    'bwd.stream.topological.degree' \tab  

+    'fwd.stream.topological.degree' \cr 

+    'bwd.stream.topological.betweenness' \tab 

+    'fwd.stream.topological.betweenness'  \cr

+    'bwd.stream.topological.closeness' \tab 

+    'fwd.stream.topological.closeness' \cr 

+    'bwd.stream.topological.hub_score' \tab 

+    'fwd.stream.topological.hub_score' \cr

+    'bwd.stream.topological.eccentricity' \tab 

+    'fwd.stream.topological.eccentricity' \cr 

+    'bwd.stream.topological.page_rank' \tab  

+    'fwd.stream.topological.page_rank' \cr

+    'bwd.stream.topological.start_nodes' \tab 

+    'fwd.stream.topological.start_nodes' \cr 

+    \tab  \cr

+    STREAM-FUNCTIONAL  \tab  \cr

+    'bwd.stream.functional.GO_bp' \tab 

+    'fwd.stream.functional.GO_bp' \cr

+    'bwd.stream.functional.GO_cc' \tab 

+    'fwd.stream.functional.GO_cc' \cr 

+    'bwd.stream.functional.GO_mf' \tab 

+    'fwd.stream.functional.GO_mf' \cr

+    'bwd.stream.functional.KEGG' \tab 

+    'fwd.stream.functional.KEGG' \cr 

+    'bwd.stream.functional.Disease_OMIM' \tab 

+    'fwd.stream.functional.Disease_OMIM' \cr

+    'bwd.stream.functional.Disease_GAD' \tab 

+    'fwd.stream.functional.Disease_GAD' \cr

+    'bwd.stream.functional.Drug_DrugBank' \tab 

+    'fwd.stream.functional.Drug_DrugBank' \cr

+    'bwd.stream.functional.miRNA' \tab 

+    'fwd.stream.functional.miRNA' \cr

+    'bwd.stream.functional.TF' \tab 

+    'fwd.stream.functional.TF' \cr

+    'bwd.stream.functional.DEG' \tab 

+    'fwd.stream.functional.DEG' \cr

+    \tab  \cr

+    NEIGHBOURHOOD-TOPOLOGICAL  \tab  \cr

+    'bwd.neighbourhood.topological.degree' \tab 

+    'fwd.neighbourhood.topological.degree' \cr

+    'bwd.neighbourhood.topological.betweenness' \tab 

+    'fwd.neighbourhood.topological.betweenness' \cr

+    'bwd.neighbourhood.topological.closeness' \tab 

+    'fwd.neighbourhood.topological.closeness' \cr

+    'bwd.neighbourhood.topological.hub_score' \tab 

+    'fwd.neighbourhood.topological.hub_score' \cr

+    'bwd.neighbourhood.topological.eccentricity' \tab 

+    'fwd.neighbourhood.topological.eccentricity' \cr

+    'bwd.neighbourhood.topological.page_rank' \tab 

+    'fwd.neighbourhood.topological.page_rank' \cr

+    'bwd.neighbourhood.topological.start_nodes' \tab 

+    'fwd.neighbourhood.topological.start_nodes' \cr

+    \tab  \cr

+    NEIGHBOURHOOD-FUNCTIONAL   \tab  \cr

+    'bwd.neighbourhood.functional.GO_bp' \tab 

+    'fwd.neighbourhood.functional.GO_bp' \cr

+    'bwd.neighbourhood.functional.GO_cc' \tab 

+    'fwd.neighbourhood.functional.GO_cc' \cr

+    'bwd.neighbourhood.functional.GO_mf' \tab 

+    'fwd.neighbourhood.functional.GO_mf' \cr

+    'bwd.neighbourhood.functional.KEGG' \tab 

+    'fwd.neighbourhood.functional.KEGG' \cr

+    'bwd.neighbourhood.functional.Disease_OMIM' \tab 

+    'fwd.neighbourhood.functional.Disease_OMIM' \cr

+    'bwd.neighbourhood.functional.Disease_GAD' \tab 

+    'fwd.neighbourhood.functional.Disease_GAD' \cr

+    'bwd.neighbourhood.functional.Drug_DrugBank' \tab 

+    'fwd.neighbourhood.functional.Drug_DrugBank' \cr

+    'bwd.neighbourhood.functional.miRNA' \tab 

+    'fwd.neighbourhood.functional.miRNA' \cr

+    'bwd.neighbourhood.functional.TF' \tab 

+    'fwd.neighbourhood.functional.DEG' \cr

+    \tab  \cr

+    CASCADE-TOPOLOGICAL  \tab  \cr

+    'bwd.cascade.topological.degree' \tab 

+    'fwd.cascade.topological.degree' \cr

+    'bwd.cascade.topological.betweenness' \tab 

+    'fwd.cascade.topological.betweenness' \cr

+    'bwd.cascade.topological.closeness' \tab 

+    'fwd.cascade.topological.closeness' \cr

+    'bwd.cascade.topological.hub_score' \tab 

+    'fwd.cascade.topological.hub_score' \cr

+    'bwd.cascade.topological.eccentricity' \tab 

+    'fwd.cascade.topological.eccentricity' \cr

+    'bwd.cascade.topological.page_rank' \tab 

+    'fwd.cascade.topological.page_rank' \cr

+    'bwd.cascade.topological.start_nodes' \tab 

+    'fwd.cascade.topological.start_nodes' \cr

+    \tab  \cr

+    \tab  \cr

+    CASCADE-FUNCTIONAL  \tab  \cr

+    'bwd.cascade.functional.GO_bp' \tab 

+    'fwd.cascade.functional.GO_bp' \cr

+    'bwd.cascade.functional.GO_cc' \tab 

+    'fwd.cascade.functional.GO_cc' \cr

+    'bwd.cascade.functional.GO_mf' \tab 

+    'fwd.cascade.functional.GO_mf' \cr

+    'bwd.cascade.functional.KEGG' \tab 

+    'fwd.cascade.functional.KEGG' \cr

+    'bwd.cascade.functional.Disease_OMIM' \tab 

+    'fwd.cascade.functional.Disease_OMIM' \cr

+    'bwd.cascade.functional.Disease_GAD' \tab 

+    'fwd.cascade.functional.Disease_GAD' \cr

+    'bwd.cascade.functional.Drug_DrugBank' \tab 

+    'fwd.cascade.functional.Drug_DrugBank' \cr

+    'bwd.cascade.functional.miRNA' \tab 'fwd.cascade.functional.miRNA' \cr

+    'bwd.cascade.functional.TF' \tab 'fwd.cascade.functional.TF' \cr

+    'bwd.cascade.functional.DEG' \tab 'fwd.cascade.functional.DEG' \cr

+    \tab  \cr

+    COMMUNITY  \tab  \cr

+    'community.walktrap' \tab 'community.edge_betweenness' \cr

+    'community.fast_greedy' \tab 'community.leading_eigen' \cr

+    'community.infomap' \tab 'community.louvain' \cr

+    \tab  \cr

+    COMPONENT-CLIQUES  \tab  \cr

+    'component.max_cliques' \tab 'component.decompose' \cr

+    'component.3-cliques' \tab ... \cr

+    ... \tab 'component.9-cliques' \cr

+    \tab  \cr

+    COMPONENT-CORENESS  \tab  \cr

+    'component.3-coreness' \tab ... \cr

+    ... \tab 'component.9-coreness' \cr

+}

+

+}

+\examples{

+

+basic.types <- subpathwayTypes()

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

+

+}

+

+

+

+

+

+

+

+