Usage
findConsensusPeakRegionsForOneChrom(chrName, allPeaks, allNarrowPeaks, extendingSize, expandToFitPeakRegion, shrinkToFitPeakRegion, minNbrExp, chrList)
Arguments
chrName
a character, the name of the chromosome to analyze.
allPeaks
a GRanges containing all peaks from all experiments
sorted by position.
allNarrowPeaks
a GRanges containing all narrow peaks from all
experiments sorted by position.
extendingSize
a numeric value indicating the size of padding
at each side of the peaks median position to create the consensus
region. The minimum size of the consensu region will be equal to
twice the value of the extendingSize parameter. The size of
the extendingSize must be a positive integer. Default = 250.
expandToFitPeakRegion
a logical indicating if the region set by
the extendingSize parameter is extended to include all narrow peak
regions. Only the narrow peaks regions of the peaks included in the
unextended region are used during the extension process. It is possible
that has a side effect, adding peaks are being included in the
extended region.
shrinkToFitPeakRegion
a logical indicating if the region set
by the extendingSize parameter is shrinked to fit the narrow
peak regions.
minNbrExp
a numeric indicating the minimum number of BED files
in which a peak must be present for a region to be retained. The
numeric must be a positive value inferior or equal to the number
of files present in the narrowPeakFiles parameter. Default = 1.
chrList
a Seqinfo containing the name and the length of the
chromosomes to analyze.