Identification of transcriptional regulatory modules from PPI networks


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Documentation for package ‘rTRM’ version 1.10.2

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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.