findDifferentialMotifs: Find Differential Motifs

In BIMSBbioinfo/RCAS: RNA Centric Annotation System

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)

BIMSBbioinfo/RCAS documentation built on Feb. 7, 2024, 4:38 p.m.