mergeRegions {htSeqTools} | R Documentation |
Merges regions that are less than maxDist
bases apart.
mergeRegions(intervals, chromosome, score, annot, aggregateFUN='median', maxDist=300)
intervals |
Object indicating start and end of each region. It
can either be a |
chromosome |
Chromosome that the region belongs to (optional). If supplied, must be of the same length as |
score |
Numerical score for each interval. Scores in merged
intervals are aggregated using function |
annot |
Character indicating annotation information for each interval. Annotations in merged intervals are pasted in a single string (annotations appearing in more than one interval are only reported once in the merged interval). |
aggregateFUN |
Function to aggregate |
maxDist |
Regions less than |
The result is returned in a data.frame
indicating the start and
end of each merged interval. If the arguments were provided, the information in
chromosome
, score
and annot
is provided in
additional columns.
If the input argument intervals
was of class RangedData
, the results are returned in a RangedData
object.
signature(intervals = "data.frame")
intervals$start
and intervals$end
give the interval start/end positions.
signature(intervals = "IRanges")
start(intervals)
and end(intervals)
give the interval start/end positions.
signature(intervals = "matrix")
The columns start
and end
in intervals
give the interval start/end positions
signature(intervals = "RangedData")
start(intervals)
and end(intervals)
give the interval start/end positions.
signature(intervals = "RleViews")
start(intervals)
and end(intervals)
give the interval start/end positions.
David Rossell
st <- c(10,20,1000) intervals <- RangedData(IRanges(st,st+10),space='chr1') intervals mergeRegions(intervals,maxDist=300)