# Identification of transcriptional regulatory modules from PPI networks

## Documentation for package ‘rTRM’ version 1.2.0

- 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.