overlap.feat: Feature overlap
In rphast: Interface to 'PHAST' Software for Comparative Genomics

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	overlap.feat(x, filter, numbase = 1, min.percent = NULL, overlapping = TRUE, get.fragments = FALSE, pointer.only = FALSE)

`x`	An object of type `feat` containing features to select
`filter`	An object of type `feat` which determines which elements of x to select
`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 `FALSE`, choose records with less than numbase overlapping bases, and less than min.percent fraction overlap if min.percent is not `NULL`
`get.fragments`	If `FALSE`, entire records are selected from x based on whether they meet selection criteria. If `TRUE`, return only the fragments of x that overlap with filter. In this case, the same fragments may be output multiple times, if they are selected by multiple entries in filter. numbase and min.percent apply in either case. When this option is used, the return value is a list with two gffs. The first (named frags) contains the overlapping fragments, and the second (filter.frags) contain the fragments from filter which selected the overlapping fragments.
`pointer.only`	If `TRUE`, the return object will only be a pointer to an object stored in C (useful for very large features; advanced use only).

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

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)