Creates a set of 2D intervals.
gintervals.2d(
chroms1 = NULL,
starts1 = 0,
ends1 = -1,
chroms2 = NULL,
starts2 = 0,
ends2 = -1
)chromosomes1 - an array of strings with or without "chr" prefixes or an array of integers (like: '1' for "chr1")
an array of start1 coordinates
an array of end1 coordinates. If '-1' chromosome size is assumed.
chromosomes2 - an array of strings with or without "chr" prefixes or an array of integers (like: '1' for "chr1"). If 'NULL', 'chroms2' is assumed to be equal to 'chroms1'.
an array of start2 coordinates
an array of end2 coordinates. If '-1' chromosome size is assumed.
A data frame representing the intervals.
This function returns a set of two-dimensional intervals. The returned value can be used in all functions that accept 'intervals' argument.
Two-dimensional intervals is a data frame whose first six columns are 'chrom1', 'start1', 'end1', 'chrom2', 'start2' and 'end2'. Each row of the data frame represents two genomic intervals from two chromosomes in the range of [start, end). Additional columns can be presented in 2D intervals object yet these columns must be added after the six obligatory ones.
gdb.init_examples()
## the following 3 calls produce identical results
gintervals.2d(1)
#> chrom1 start1 end1 chrom2 start2 end2
#> 1 chr1 0 5e+05 chr1 0 5e+05
gintervals.2d("1")
#> chrom1 start1 end1 chrom2 start2 end2
#> 1 chr1 0 5e+05 chr1 0 5e+05
gintervals.2d("chrX")
#> chrom1 start1 end1 chrom2 start2 end2
#> 1 chrX 0 2e+05 chrX 0 2e+05
gintervals.2d(1, 1000, 2000, "chrX", 400, 800)
#> chrom1 start1 end1 chrom2 start2 end2
#> 1 chr1 1000 2000 chrX 400 800
gintervals.2d(c("chr2", "chrX"), 10, c(3000, 5000), 1)
#> chrom1 start1 end1 chrom2 start2 end2
#> 1 chr2 10 3000 chr1 0 5e+05
#> 2 chrX 10 5000 chr1 0 5e+05