coverage.feat: Features coverage
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Value Note Author(s) Examples

Features coverage

1 2	coverage.feat(..., or = FALSE, not = FALSE, get.feats = FALSE, pointer.only = FALSE)

`...`	objects of type `feat`
`or`	if `TRUE`, get the coverage of union of feat arguments. or is `FALSE` by default, which takes the intersection.
`not`	If not `NULL`, a vector of logicals the same length as the number of features provided (or will be recycled to this length). For each value which is `TRUE`, then any base not included in this feature will be counted. (The negation is done before any other operation). If `NULL`, do not negate any features. There must be at least one feature which is not negated (so that boundaries can be established).
`get.feats`	if `TRUE`, return an object of type `feat` representing the intersection (or union of `or==TRUE`) of the features
`pointer.only`	(Only used if `get.feats==TRUE`). If `TRUE`, the features object returned will be stored as a pointer to an object in C.

The number of bases covered by the feat arguments, or the combined feat object if get.feats==TRUE.

Any features object passed into this function which is stored as a pointer to an object stored in C may be reordered (sorted) by this function.

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))
coverage.feat(feat1, feat2, or=FALSE)
coverage.feat(feat1, feat2, or=TRUE)
coverage.feat(feat1, feat2, get.feats=TRUE, or=TRUE)
coverage.feat(feat1, feat2, or=TRUE)
rm(feat1, feat2)