misha (version 4.2.9)

gintervals.force_range: Limits intervals to chromosomal range

Description

Limits intervals to chromosomal range.

Usage

gintervals.force_range(intervals = NULL, intervals.set.out = NULL)

Value

If 'intervals.set.out' is 'NULL' a data frame representing the intervals.

Arguments

intervals

intervals

intervals.set.out

intervals set name where the function result is optionally outputted

Details

This function enforces the intervals to be within the chromosomal range [0, chrom length) by altering the intervals' boundaries. Intervals that lay entirely outside of the chromosomal range are eliminated. The new intervals are returned.

If 'intervals.set.out' is not 'NULL' the result is saved as an intervals set. Use this parameter if the result size exceeds the limits of the physical memory.

See Also

gintervals, gintervals.2d, gintervals.canonic

Examples

# \dontshow{
options(gmax.processes = 2)
# }

gdb.init_examples()
intervs <- data.frame(
    chrom = "chr1",
    start = c(11000, -100, 10000, 10500),
    end = c(12000, 200, 13000000, 10600)
)
gintervals.force_range(intervs)