runMotifRG {RCAS} | R Documentation

## runMotifRG

### Description

This function makes use of `motifRG` library to carry out de novo motif discovery from input query regions

### Usage

    runMotifRG(queryRegions, resizeN = 0, sampleN = 0, genomeVersion,
      motifN = 5, nCores = 4)

### Arguments

`queryRegions` | GRanges object containing coordinates of input query regions imported by the `importBed` function
`resizeN` | Integer value (default: 0) to resize query regions if they are shorter than the value of `resize`. Set to 0 to disable resize.
`sampleN` | A positive integer value. The queryRegions are randomly downsampled to include intervals as many as `sampleN`. The input will be downsampled only if this value is larger than zero and less than the total number of input intervals.
`genomeVersion` | A character string to denote the BS genome library required to extract sequences. Available options are hg19, mm9, ce10 and dm3.
`motifN` | A positive integer (default:5) denoting the maximum number of motifs that should be sought by the `motifRG::findMotifFgBg` function
`nCores` | A positive integer (default:4) number of cores used for parallel execution.

### Value

a list of objects returned by the `motifRG::findMotif` function

### Examples

    data(queryRegions)
    motifResults <- runMotifRG(queryRegions = queryRegions,
                              genomeVersion = 'hg19',
                              resize = 15,
                              motifN = 1,
                              nCores = 2)

[Package RCAS version 1.12.0 Index]