Creates a set of 1D intervals

Creates a set of 1D intervals.

gintervals(chroms = NULL, starts = 0, ends = -1, strands = NULL)

Arguments

chroms

chromosomes - an array of strings with or without "chr" prefixes or an array of integers (like: '1' for "chr1")

starts

an array of start coordinates

ends

an array of end coordinates. If '-1' chromosome size is assumed.

strands

'NULL' or an array consisting of '-1', '0' or '1' values

Value

A data frame representing the intervals.

Details

This function returns a set of one-dimensional intervals. The returned value can be used in all functions that accept 'intervals' argument.

One-dimensional intervals is a data frame whose first three columns are 'chrom', 'start' and 'end'. Each row of the data frame represents a genomic interval of the specified chromosome in the range of [start, end). Additional columns can be presented in 1D intervals object yet these columns must be added after the three obligatory ones.

If 'strands' argument is not 'NULL' an additional column "strand" is added to the intervals. The possible values of a strand can be '1' (plus strand), '-1' (minus strand) or '0' (unknown).

See also

gintervals.2d, gintervals.force_range

Examples

gdb.init_examples()

## the following 3 calls produce identical results
gintervals(1)
#>   chrom start   end
#> 1  chr1     0 5e+05
gintervals("1")
#>   chrom start   end
#> 1  chr1     0 5e+05
gintervals("chrX")
#>   chrom start   end
#> 1  chrX     0 2e+05

gintervals(1, 1000)
#>   chrom start   end
#> 1  chr1  1000 5e+05
gintervals(c("chr2", "chrX"), 10, c(3000, 5000))
#>   chrom start  end
#> 1  chr2    10 3000
#> 2  chrX    10 5000