Man pages for rTRM
Identification of transcriptional regulatory modules from PPI networks

annotateFreqAnnotate a graph with frequency of nodes/edges in other...
annotateModuleAnnotate a network module with information
annotateTRMAnnotate a network object with information about clusters.
biogrid_hsNetwork dataset of class 'igraph'
biogrid_mmNetwork dataset of class 'igraph'
findTRMIndentifies a TRM associated with a target node and one or...
getAnnotationsObtain the 'pwm' table fromt the database, containing PWM's...
getBiogridDataDownloads network data from BioGRID in TAB2 format.
getConcentricListReturns a list with nodes membership to be used in a graph...
getLargestCompGets the largest connected component
getMapsObtain the mapping between PWM and Entrez Gene identifiers.
getMatricesObtain a list of PWMs.
getMotifsFromEntrezgeneRetrieve PWMs associated with genes provided as entrezgene...
getMotifsFromSymbolRetrieve PWMs associated with genes provided as symbol.
getOrthologFromMatrixObtain gene identifiers for a target organism associated with...
getOrthologsObtain the mapping to Entrez Gene identifiers in the given...
getOrthologsFromBiomartReturns ortholog genes for a target organism
getSequencesFromGenomeRetrieves a set of sequences from a BSgenome object and...
getSimilarityMatrixCompute similarity matrix of list of graphs.
getTFclassReturn the ontology in the TFclass database associated with...
getTFclassFromEntrezgeneApplies getTFclass sequentially to a vector of entrezgene...
getTFtermsGet terms associated with a specified TFclass subset.
initBiomartInitializes mart objects to identify ortholog genes
layout.arcLayouts a graph using arcs.
layout.concentricGenerates a concentric layout for graphs
plotDegreePlot degree distribution for network nodes
plotGraphPlot an graph in igraph format.
plotTRMPlot an annotated TRM.
plotTRMlegendPlot the legend of a TRM with information about the cluster...
processBiogridProcess a data.frame with BioGRID data into a network for a...
removeVerticesRemove nodes from a graph and returns the largest component
rTRM-packageIdentification transcription regulatory modules (TRMs)
writeTRMreportExport a table with TRM nodes and associated information.
rTRM documentation built on Nov. 17, 2017, 8:20 a.m.