Creates 1D intervals from coordinate strings

Creates a set of 1D intervals by parsing UCSC-style coordinate strings.

gintervals.from_strings(regions = NULL)

Arguments

regions

a character vector of region strings. Accepted formats per element: "chrom", "chrom:start-end", "chrom:start..end", optionally followed by ":+" or ":-".

Value

A data frame representing the intervals, sorted as by gintervals. A "strand" column is added only when at least one region specifies a strand.

Details

Parses strings of the form "chrom:start-end" ("chrom:start..end" is also accepted) into a 1D intervals data frame. A chromosome-only string such as "chr1" expands to the full chromosome extent. An optional trailing strand suffix ":+" or ":-" adds a "strand" column.

Coordinates are zero-based and half-open, matching the convention used by gintervals.

See also

gintervals, gintervals.2d

Examples

gdb.init_examples()
gintervals.from_strings("chr1:1000-2000")
#>   chrom start  end
#> 1  chr1  1000 2000
gintervals.from_strings(c("chr1:1000-2000:+", "chr2:50-60:-"))
#>   chrom start  end strand
#> 1  chr1  1000 2000      1
#> 2  chr2    50   60     -1