rphast (version 1.0)

coverage.feat: Features coverage...

Description

Features coverage

Usage

coverage.feat(..., or=FALSE, get.feats=FALSE, not=NULL,
    region.bounds=NULL)

Arguments

...

objects of type feat

or

if TRUE, get the coverage of union of feat arguments. or is FALSE by default, which takes the intersection.

get.feats

if TRUE, return an object of type feat representing the intersection (or union of or==TRUE) of the features.

not

If not NULL, a vector of logicals the same length as the number of features provided. For each value which is TRUE, the inverse of the feature will be used. If any element of not is TRUE, then the regi

region.bounds

An object of type feat which defines the start and end coordinates of all relevant chromosomes/regions in the provided feat objects. Used for taking inverses of the feat objects as required by the argument not. If not==NU

Value

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

Examples

require("rphast")
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)