gintervals: Creates a set of 1D intervals

In misha: Toolkit for Analysis of Genomic Data

Creates a set of 1D intervals

Description

Creates a set of 1D intervals.

Usage

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

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).

Value

A data frame representing the intervals.

See Also

gintervals.2d, gintervals.force_range

Examples

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))

misha documentation built on Sept. 14, 2023, 5:08 p.m.