gintervals: Creates a set of 1D intervals

Description

Creates a set of 1D intervals.

Usage

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

Value

A data frame representing the intervals, sorted in the canonical chromosome order (which is not the order of the arguments). Beware of keeping per-interval data in a separate parallel vector across a gintervals()

call: the rows are reordered and the vector is not. Put such data in a column of the resulting data frame instead.

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', a numeric vector of '-1', '0' or '1' values, or a character/factor vector with values "+", "-", ".", "*" or ""

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). Character values "+", "-", ".", "*" and "" (or factors with these levels) are also accepted and converted internally to '1', '-1' and '0' respectively.

Examples

Run this code

# \dontshow{
options(gmax.processes = 2)
# }

gdb.init_examples()

## the following 3 calls produce identical results
gintervals(1)
gintervals("1")
gintervals("chrX")

gintervals(1, 1000)
gintervals(c("chr2", "chrX"), 10, c(3000, 5000))