findDifferentialMotifs {RCAS} | R Documentation |
Find Differential Motifs
findDifferentialMotifs( querySeqs, controlSeqs, motifWidth = 6, motifN = 1, nCores = 1, maxMismatch = 1 )
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 |
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. |
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)