runMotifRG {RCAS} | R Documentation |
This function makes use of motifRG
library to carry out de novo motif
discovery from input query regions
runMotifRG(queryRegions, resizeN = 0, sampleN = 0, genomeVersion, motifN = 5, nCores = 4)
queryRegions |
GRanges object containing coordinates of input query
regions imported by the |
resizeN |
Integer value (default: 0) to resize query regions if they are
shorter than the value of |
sampleN |
A positive integer value. The queryRegions are randomly
downsampled to include intervals as many as |
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 |
nCores |
A positive integer (default:4) number of cores used for parallel execution. |
a list of objects returned by the motifRG::findMotif
function
data(queryRegions) motifResults <- runMotifRG(queryRegions = queryRegions, genomeVersion = 'hg19', resize = 15, motifN = 1, nCores = 2)