RangesList-methods {rtracklayer}R Documentation

Ranges on a Genome

Description

Genomic coordinates are often specified in terms of a genome identifier, chromosome name, start position and end position. This information can be represented by a RangesList instance, and the rtracklayer package adds convenience methods to RangesList for the manipulation of genomic ranges. The spaces (or names) of RangesList are the chromosome names. The universe slot indicates the genome, usually as given by UCSC (e.g. “hg18”).

Accessors

In the code snippets below, x is a RangesList object.

chrom(x): Gets the chromosome names (a factor) over the ranges in x.
genome(x), genome(x) <- value: Gets or sets the genome (a single string or NULL) for the ranges in x; simple wrappers around universe and universe<-, respectively.

Constructor

GenomicRanges(start, end, chrom = NULL, genome = NULL): Constructs a RangesList containing ranges specified by start and end, optionally split into elements based on chrom, a vector of chromosome identifiers (or NULL for no splitting). The genome argument should be a scalar string and is treated as the RangesList universe. See the examples.

Author(s)

Michael Lawrence

Examples

GenomicRanges(c(1,2,3), c(5,2,8))
GenomicRanges(c(1,2,3), c(5,2,8), c("chr1", "chr1", "chr2"))
GenomicRanges(c(1,2,3), c(5,2,8), genome = "hg18")

[Package rtracklayer version 1.4.1 Index]