discoverFeatureSpecificMotifs: discoverFeatureSpecificMotifs

In RCAS: RNA Centric Annotation System

Description

This function groups query regions based on their overlap with different transcript features and generates a table of top enriched motif and matching patterns for each given transcript feature type along with some other motif discovery related statistics.

Usage

discoverFeatureSpecificMotifs(queryRegions, txdbFeatures, ...)

Arguments

queryRegions	GRanges object containing coordinates of input query regions imported by the importBed function
txdbFeatures	A list of GRanges objects where each GRanges object corresponds to the genomic coordinates of gene features such as promoters, introns, exons, 5'/3' UTRs and whole transcripts. This list of GRanges objects are obtained by the function getTxdbFeaturesFromGRanges or getTxdbFeatures.
...	Other arguments passed to runMotifRG function. Important arguments are 'genomeVersion' and motifN. If motifN is bigger than 1, then multiple motifs will be found but only the top motif will be plotted.

Value

A data.frame object

Examples

## Not run: 
data(gff)
data(queryRegions)
txdbFeatures <- getTxdbFeaturesFromGRanges(gffData = gff)
discoverFeatureSpecificMotifs(queryRegions = queryRegions, 
genomeVersion = 'hg19', txdbFeatures = txdbFeatures, 
motifN = 1, nCores = 1)
## End(Not run)

RCAS documentation built on Nov. 8, 2020, 8:03 p.m.