findDifferentialMotifs {RCAS} | R Documentation

## Find Differential Motifs

### Description

Find Differential Motifs

### Usage

    findDifferentialMotifs(
      querySeqs,
      controlSeqs,
      motifWidth = 6,
      motifN = 1,
      nCores = 1,
      maxMismatch = 1
    )

### Arguments

`querySeqs` | A DNAStringSet object that is the regions of interest.
`controlSeqs` | A DNAStrintSet object that serve as the control
`motifWidth` | A Positive integer (default: 6) for the generated k-mers. Warning: we recommend using values below 10 as the computation gets exponentially difficult as the motif width is increased.
`motifN` | A positive integer (default:1) denoting the maximum number of motifs that should be returned by the `findDifferentialMotifs` function
`nCores` | A positive integer (default:1) number of cores used for parallel execution.
`maxMismatch` | A positive integer (default: 1) - maximum number of mismatches to allow when searching for k-mer matches in sequences.

### Examples

    data(queryRegions)

    # get query and control sequences
    querySeqs <- extractSequences(queryRegions[1:500], 'hg19')
    controlRegions <- createControlRegions(queryRegions[1:500])
    controlSeqs <- extractSequences(controlRegions, 'hg19')

    #run motif discovery
    motifResults <- findDifferentialMotifs(querySeqs = querySeqs,
                                           controlSeqs = controlSeqs,
                                           motifWidth = 5,
                                           motifN = 1,
                                           maxMismatch = 0,
                                           nCores = 1)
    #summarize motif results
    getMotifSummaryTable(motifResults)

[Package RCAS version 1.16.0 Index]