mapMotifsToTFsMergeIntoTable: Map Motifs to Transcription Factors and Merge into a Table

In TReNA: Fit transcriptional regulatory networks using gene expression, priors, machine learning

Description

Using the motifsgenes table inside the genome database specified by the FootprintFinder object, return a table mapping each motif to transcription factors

Usage

## S4 method for signature 'FootprintFinder'
mapMotifsToTFsMergeIntoTable(obj, tbl)

Arguments

obj	An object of class FootprintFinder
tbl	A dataframe of footprints, generally obtained using getFootprintsInRegion or getFootprintsForGene

Value

A data frame containing the motifs from the supplied footprints table and the transcription factors they map to

See Also

Other FootprintFinder methods: FootprintFinder-class, closeDatabaseConnections,FootprintFinder-method, getChromLoc,FootprintFinder-method, getFootprintsForGene,FootprintFinder-method, getFootprintsInRegion,FootprintFinder-method, getGenePromoterRegion,FootprintFinder-method, getGtfGeneBioTypes,FootprintFinder-method, getGtfMoleculeTypes,FootprintFinder-method, getPromoterRegionsAllGenes,FootprintFinder-method

Examples

db.address <- system.file(package="TReNA", "extdata")
genome.db.uri <- paste("sqlite:/",db.address,"genome.sub.db", sep = "/")
project.db.uri <- paste("sqlite:/",db.address,"project.sub.db", sep = "/")
fp <- FootprintFinder(genome.db.uri, project.db.uri)

footprints <- getFootprintsForGene(fp, gene = "MEF2C")
tfs <- mapMotifsToTFsMergeIntoTable(fp, footprints)

TReNA documentation built on Nov. 17, 2017, 12:35 p.m.