Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks

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Documentation for package ‘rTRM’ version 1.45.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

rTRM-package	Identification transcription regulatory modules (TRMs)
annotateFreq	Annotate a graph with frequency of nodes/edges in other graphs.
annotateModule	Annotate a network module with information
annotateTRM	Annotate a network object with information about clusters.
biogrid_hs	Network dataset of class 'igraph'
biogrid_mm	Network dataset of class 'igraph'
findTRM	Indentifies a TRM associated with a target node and one or more query nodes.
getAnnotations	Obtain the 'pwm' table fromt the database, containing PWM's annotations.
getBiogridData	Downloads network data from BioGRID in TAB2 format.
getConcentricList	Returns a list with nodes membership to be used in a graph with a concentric layout
getLargestComp	Gets the largest connected component
getMaps	Obtain the mapping between PWM and Entrez Gene identifiers.
getMatrices	Obtain a list of PWMs.
getMotifsFromEntrezgene	Retrieve PWMs associated with genes provided as entrezgene identifiers.
getMotifsFromSymbol	Retrieve PWMs associated with genes provided as symbol.
getOrthologFromMatrix	Obtain gene identifiers for a target organism associated with a list of PWMs.
getOrthologs	Obtain the mapping to Entrez Gene identifiers in the given organism.
getOrthologsFromBiomart	Returns ortholog genes for a target organism
getSequencesFromGenome	Retrieves a set of sequences from a BSgenome object and optionally appends a label to each sequence id.
getSimilarityMatrix	Compute similarity matrix of list of graphs.
getTFclass	Return the ontology in the TFclass database associated with an entrezgene identifier
getTFclassFromEntrezgene	Applies getTFclass sequentially to a vector of entrezgene identifiers.
getTFterms	Get terms associated with a specified TFclass subset.
initBiomart	Initializes mart objects to identify ortholog genes
layout.arc	Layouts a graph using arcs.
layout.concentric	Generates a concentric layout for graphs
plotDegree	Plot degree distribution for network nodes
plotGraph	Plot an graph in igraph format.
plotTRM	Plot an annotated TRM.
plotTRMlegend	Plot the legend of a TRM with information about the cluster families.
processBiogrid	Process a data.frame with BioGRID data into a network for a target organism
removeVertices	Remove nodes from a graph and returns the largest component
rTRM	Identification transcription regulatory modules (TRMs)
writeTRMreport	Export a table with TRM nodes and associated information.