Browse code

Adding FitHiC, SIMLR, SPLINTER, GOpro, DEsubs, statTarget, CancerInSilico, geneXtendeR

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEsubs@122029 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 07/10/2016 08:32:34
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+\name{subpathwayTypes}
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+\alias{subpathwayTypes}
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+\title{All subpathway types}
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+\usage{
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+subpathwayTypes(grouping)
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+}
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+\arguments{
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+\item{grouping}{By supplying one of the availiable groupings, specific 
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+subsets of availiable subpathway types can be extracted.}
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+}
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+\value{
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+A vector of all 124 basic subpathway types. See Details section for handly 
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+groupings.
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+}
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+\description{
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+All subpathway types.
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+}
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+\details{
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+Apart from the 124 distinct subpathway types, several groupings are availiable:
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+\describe{
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+\item{'all'}{ All subpathway options. }
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+\item{'all.bwd'}{ Forward propagation. }
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+\item{'all.fwd'}{Backward propagation. }
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+\item{'all.stream'}{All possible genes targeting or are targeted 
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+via a path starting from a gene of interest.}
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+\item{'all.neighbourhood'}{All adjacent genes of a gene of interest with 
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+incoming or outgoing links.}
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+\item{'all.cascade'}{A finite sequence of interactions connecting a sequence 
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+of genes starting or ending from a gene of interest.}
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+\item{'all.community'}{Group of genes sharing common properties.}
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+\item{'all.component'}{Subgraphs on which any two vertices are (strongly)
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+connected to each other by paths.}
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+\item{ }{}
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+\item{'all.functional'}{Forward and backward streams starting from 
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+genes/nodes with crucial functional role within the network. Individual 
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+options include GO_bp, GO_cc, GO_mf, KEGG, Disease_OMIM, Disease_GAD, 
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+Drug_DrugBank, miRNA, TF, DEG, which are defined below.}
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+\item{'all.GO_bp'}{Genes acting as a bridge among Gene Ontology (GO) 
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+Biological Process terms. }
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+\item{'all.GO_cc'}{Genes acting as a bridge among Gene Ontology (GO) 
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+Cellular Component terms. }
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+\item{'all.GO_mf'}{Genes acting as a bridge among Gene Ontology (GO) 
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+Molecular Function terms. }
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+\item{'all.KEGG'}{Genes acting as a bridge among KEGG pathway maps. }
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+\item{'all.Disease_OMIM'}{Genes acting as a bridge among OMIM Disease 
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+targets.}
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+\item{'all.Disease_GAD'}{Genes acting as a bridge among GAD Disease targets.}
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+\item{'all.Drug_DrugBank'}{Genes acting as a bridge among DrugBank Drug 
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+targets.}
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+\item{'all.miRNA'}{Genes acting as a bridge among microRNA-gene targets. }
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+\item{'all.TF'}{Genes acting as a bridge among TF-gene targets. }
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+\item{'all.DEG'}{Genes with highly Differentially expressed by each 
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+experimental data. }
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+\item{}{}
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+\item{'all.topological'}{Forward and backward streams starting from 
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+genes/nodes with crucial topological role within the network. Individual 
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+options include degree, betweenness, closeness, hub_score, eccentricity, 
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+page_rank, start_nodes which are defined below.}
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+\item{'all.degree'}{Number of gene's adjacent interactions.}
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+\item{'all.betweenness'}{Number of shortest paths from all vertices to  
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+others passing through a node.}
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+\item{'all.closeness'}{Inverse of farness, which is the sum of distances 
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+to all other nodes.}
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+\item{'all.hub_score'}{Kleinberg's hub centrality score.}
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+\item{'all.eccentricity'}{Shortest path distance from the farthest other 
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+node in the graph.}
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+\item{'all.page_rank'}{Google Page Rank.}
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+\item{'all.start_nodes'}{Gene nodes without incoming links.}
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+\item{}{}
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+}
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+
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+An exhaustive list of all 124 subpathway types follows:
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+
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+\tabular{ll}{
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+    \tab  \cr
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+    STREAM-TOPOLOGICAL  \tab  \cr
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+    'bwd.stream.topological.degree' \tab  
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+    'fwd.stream.topological.degree' \cr 
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+    'bwd.stream.topological.betweenness' \tab 
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+    'fwd.stream.topological.betweenness'  \cr
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+    'bwd.stream.topological.closeness' \tab 
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+    'fwd.stream.topological.closeness' \cr 
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+    'bwd.stream.topological.hub_score' \tab 
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+    'fwd.stream.topological.hub_score' \cr
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+    'bwd.stream.topological.eccentricity' \tab 
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+    'fwd.stream.topological.eccentricity' \cr 
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+    'bwd.stream.topological.page_rank' \tab  
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+    'fwd.stream.topological.page_rank' \cr
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+    'bwd.stream.topological.start_nodes' \tab 
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+    'fwd.stream.topological.start_nodes' \cr 
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+    \tab  \cr
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+    STREAM-FUNCTIONAL  \tab  \cr
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+    'bwd.stream.functional.GO_bp' \tab 
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+    'fwd.stream.functional.GO_bp' \cr
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+    'bwd.stream.functional.GO_cc' \tab 
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+    'fwd.stream.functional.GO_cc' \cr 
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+    'bwd.stream.functional.GO_mf' \tab 
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+    'fwd.stream.functional.GO_mf' \cr
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+    'bwd.stream.functional.KEGG' \tab 
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+    'fwd.stream.functional.KEGG' \cr 
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+    'bwd.stream.functional.Disease_OMIM' \tab 
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+    'fwd.stream.functional.Disease_OMIM' \cr
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+    'bwd.stream.functional.Disease_GAD' \tab 
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+    'fwd.stream.functional.Disease_GAD' \cr
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+    'bwd.stream.functional.Drug_DrugBank' \tab 
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+    'fwd.stream.functional.Drug_DrugBank' \cr
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+    'bwd.stream.functional.miRNA' \tab 
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+    'fwd.stream.functional.miRNA' \cr
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+    'bwd.stream.functional.TF' \tab 
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+    'fwd.stream.functional.TF' \cr
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+    'bwd.stream.functional.DEG' \tab 
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+    'fwd.stream.functional.DEG' \cr
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+    \tab  \cr
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+    NEIGHBOURHOOD-TOPOLOGICAL  \tab  \cr
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+    'bwd.neighbourhood.topological.degree' \tab 
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+    'fwd.neighbourhood.topological.degree' \cr
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+    'bwd.neighbourhood.topological.betweenness' \tab 
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+    'fwd.neighbourhood.topological.betweenness' \cr
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+    'bwd.neighbourhood.topological.closeness' \tab 
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+    'fwd.neighbourhood.topological.closeness' \cr
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+    'bwd.neighbourhood.topological.hub_score' \tab 
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+    'fwd.neighbourhood.topological.hub_score' \cr
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+    'bwd.neighbourhood.topological.eccentricity' \tab 
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+    'fwd.neighbourhood.topological.eccentricity' \cr
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+    'bwd.neighbourhood.topological.page_rank' \tab 
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+    'fwd.neighbourhood.topological.page_rank' \cr
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+    'bwd.neighbourhood.topological.start_nodes' \tab 
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+    'fwd.neighbourhood.topological.start_nodes' \cr
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+    \tab  \cr
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+    NEIGHBOURHOOD-FUNCTIONAL   \tab  \cr
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+    'bwd.neighbourhood.functional.GO_bp' \tab 
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+    'fwd.neighbourhood.functional.GO_bp' \cr
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+    'bwd.neighbourhood.functional.GO_cc' \tab 
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+    'fwd.neighbourhood.functional.GO_cc' \cr
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+    'bwd.neighbourhood.functional.GO_mf' \tab 
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+    'fwd.neighbourhood.functional.GO_mf' \cr
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+    'bwd.neighbourhood.functional.KEGG' \tab 
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+    'fwd.neighbourhood.functional.KEGG' \cr
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+    'bwd.neighbourhood.functional.Disease_OMIM' \tab 
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+    'fwd.neighbourhood.functional.Disease_OMIM' \cr
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+    'bwd.neighbourhood.functional.Disease_GAD' \tab 
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+    'fwd.neighbourhood.functional.Disease_GAD' \cr
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+    'bwd.neighbourhood.functional.Drug_DrugBank' \tab 
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+    'fwd.neighbourhood.functional.Drug_DrugBank' \cr
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+    'bwd.neighbourhood.functional.miRNA' \tab 
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+    'fwd.neighbourhood.functional.miRNA' \cr
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+    'bwd.neighbourhood.functional.TF' \tab 
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+    'fwd.neighbourhood.functional.DEG' \cr
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+    \tab  \cr
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+    CASCADE-TOPOLOGICAL  \tab  \cr
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+    'bwd.cascade.topological.degree' \tab 
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+    'fwd.cascade.topological.degree' \cr
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+    'bwd.cascade.topological.betweenness' \tab 
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+    'fwd.cascade.topological.betweenness' \cr
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+    'bwd.cascade.topological.closeness' \tab 
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+    'fwd.cascade.topological.closeness' \cr
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+    'bwd.cascade.topological.hub_score' \tab 
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+    'fwd.cascade.topological.hub_score' \cr
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+    'bwd.cascade.topological.eccentricity' \tab 
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+    'fwd.cascade.topological.eccentricity' \cr
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+    'bwd.cascade.topological.page_rank' \tab 
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+    'fwd.cascade.topological.page_rank' \cr
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+    'bwd.cascade.topological.start_nodes' \tab 
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+    'fwd.cascade.topological.start_nodes' \cr
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+    \tab  \cr
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+    \tab  \cr
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+    CASCADE-FUNCTIONAL  \tab  \cr
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+    'bwd.cascade.functional.GO_bp' \tab 
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+    'fwd.cascade.functional.GO_bp' \cr
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+    'bwd.cascade.functional.GO_cc' \tab 
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+    'fwd.cascade.functional.GO_cc' \cr
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+    'bwd.cascade.functional.GO_mf' \tab 
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+    'fwd.cascade.functional.GO_mf' \cr
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+    'bwd.cascade.functional.KEGG' \tab 
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+    'fwd.cascade.functional.KEGG' \cr
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+    'bwd.cascade.functional.Disease_OMIM' \tab 
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+    'fwd.cascade.functional.Disease_OMIM' \cr
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+    'bwd.cascade.functional.Disease_GAD' \tab 
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+    'fwd.cascade.functional.Disease_GAD' \cr
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+    'bwd.cascade.functional.Drug_DrugBank' \tab 
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+    'fwd.cascade.functional.Drug_DrugBank' \cr
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+    'bwd.cascade.functional.miRNA' \tab 'fwd.cascade.functional.miRNA' \cr
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+    'bwd.cascade.functional.TF' \tab 'fwd.cascade.functional.TF' \cr
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+    'bwd.cascade.functional.DEG' \tab 'fwd.cascade.functional.DEG' \cr
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+    \tab  \cr
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+    COMMUNITY  \tab  \cr
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+    'community.walktrap' \tab 'community.edge_betweenness' \cr
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+    'community.fast_greedy' \tab 'community.leading_eigen' \cr
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+    'community.infomap' \tab 'community.louvain' \cr
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+    \tab  \cr
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+    COMPONENT-CLIQUES  \tab  \cr
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+    'component.max_cliques' \tab 'component.decompose' \cr
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+    'component.3-cliques' \tab ... \cr
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+    ... \tab 'component.9-cliques' \cr
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+    \tab  \cr
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+    COMPONENT-CORENESS  \tab  \cr
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+    'component.3-coreness' \tab ... \cr
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+    ... \tab 'component.9-coreness' \cr
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+}
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+
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+}
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+\examples{
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+
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+basic.types <- subpathwayTypes()
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+stream.types <- subpathwayTypes(grouping='all.stream')
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+
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+}
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+
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+
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+
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+
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+
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+
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+
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+