rphast (version 1.6.9)

overlap.feat: Feature overlap

Description

Creates a features object containing all the features from one set which overlap features from another.

Usage

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

Arguments

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).

Value

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).

Examples

# NOT RUN {
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)
# }