Limits intervals to chromosomal range

Limits intervals to chromosomal range.

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

Arguments

intervals

intervals

intervals.set.out

intervals set name where the function result is optionally outputted

Value

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

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)
#>   chrom start    end
#> 1  chr1 11000  12000
#> 2  chr1     0    200
#> 3  chr1 10000 500000
#> 4  chr1 10500  10600