Description Usage Arguments Value Note Author(s) Examples
Creates a features object containing all the features from one set which overlap features from another.
1 2 |
x |
An object of type |
filter |
An object of type |
numbase |
The number of bases of overlap between x and filter required to choose a record. Use NULL to ignore (but then min.percent must be defined) |
min.percent |
The minimum percent that a record must overlap with the combined records in filter in order to be chosen |
overlapping |
If |
get.fragments |
If |
pointer.only |
If |
an object of type feat
containing the selected entries from x (unless
get.fragments==TRUE, then it returns a list with two feat
objects; see
get.fragments).
If either x or filter are feature objects stored as a pointer to C memory, then this function may reorder the elements in these objects, but leave them otherwise unchanged.
Melissa J. Hubisz
1 2 3 4 5 6 7 8 9 10 11 12 13 | feat1 <- feat(seqname=c(rep("chr1", 3), rep("chr2", 2)),
start=c(1, 5, 100, 10, 20),
end=c(7, 10, 105, 15, 30))
feat2 <- feat(seqname=c("chr1","chr2"),
start=c(1,1),
end=c(5,10))
overlap.feat(feat1, feat1)
overlap.feat(feat1, feat2, min.percent=0.25)
overlap.feat(feat1, feat2, min.percent=0.25, overlapping=FALSE)
overlap.feat(feat1, feat2, get.fragments=TRUE)
overlap.feat(feat1, feat2, get.fragments=TRUE)
rm(feat1, feat2)
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