man/subpathwayTypes.Rd
747f1150
 
 
 \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')
 
 }