Hi,
I have multiple IRanges separated by certain distance which I would like
to merge by REDUCE with the parameter min.gapwidth. If an IRange is
within the min.gapwidth, but the coverage is too low, say, only 1 or 2
across, I'd like to skip it, ie, do not perform REDUCE. Could anyone
suggest a good way to do it? Thanks.
-Kunbin
Example like the following:
> x<-IRanges(c(1,1,2,3,3,7,10,10,11), c(2,3,3,4,5,8,11,12,13))
> x
IRanges of length 9
start end width
[1] 1 2 2
[2] 1 3 3
[3] 2 3 2
[4] 3 4 2
[5] 3 5 3
[6] 7 8 2
[7] 10 11 2
[8] 10 12 3
[9] 11 13 3
> coverage(x)
'integer' Rle of length 13 with 12 runs
Lengths: 1 1 1 1 1 1 2 1 1 1 1 1
Values : 2 3 4 2 1 0 1 0 2 3 2 1
> xr<-reduce(x, min.gapwidth=2)
> xr
IRanges of length 1
start end width
[1] 1 13 13
IRange No. 6 is the weak link with a coverage of 1 in the middle, but it
links IRanges 1 to 5 with IRanges 7 to 9 to cause only one IRange after
REDUCE.
I'd like to avoid this, so REDUCE will result two clusters, one from
IRanges 1 to 5, another from IRanges 7 to 9.
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