discoverFeatureSpecificMotifs {RCAS} | R Documentation

## discoverFeatureSpecificMotifs

### 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)

[Package RCAS version 1.4.4 Index]