Loads a named intervals set

Loads a named intervals set.

gintervals.load(
  intervals.set = NULL,
  chrom = NULL,
  chrom1 = NULL,
  chrom2 = NULL
)

Arguments

intervals.set

name of an intervals set

chrom

chromosome for 1D intervals set

chrom1

first chromosome for 2D intervals set

chrom2

second chromosome for 2D intervals set

Value

A data frame representing the intervals.

Details

This function loads and returns intervals stored in a named intervals set.

If intervals set contains 1D intervals and 'chrom' is not 'NULL' only the intervals of the given chromosome are returned.

Likewise if intervals set contains 2D intervals and 'chrom1', 'chrom2' are not 'NULL' only the intervals of the given pair of chromosomes are returned.

For big intervals sets 'chrom' parameter (1D case) / 'chrom1', 'chrom2' parameters (2D case) must be specified. In other words: big intervals sets can be loaded only by chromosome or chromosome pair.

See also

gintervals.save, gintervals.is.bigset, gintervals.exists, gintervals.ls, gintervals, gintervals.2d

Examples

gdb.init_examples()
gintervals.load("annotations")
#>   chrom start   end strand  remark
#> 1  chr1    20  2000      1 remarkA
#> 5  chr1  2500  2600      1 remarkE
#> 2  chr2    20  2000      1 remarkB
#> 3  chr2  3000  8000     -1 remarkC
#> 4  chr2  9000 11000      1 remarkD
#> 6  chr2 12000 12001      1 remarkF
#> 7  chr2 13000 14000     -1 remarkG
#> 8  chr2 15000 15500      1 remarkH