Ranges on a Genome

Description

Genomic coordinates are often specified in terms of a genome identifier, chromosome name, start position and end position. RangedData represents this with 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), chrom(x) <- value: Gets or sets the chromosome names for x. This is an alias for names(x).

seqinfo(x), seqinfo(x) <- value: Gets or sets the sequence information as a Seqinfo object. If this has not been set explicitly, it tries to come up with a reasonable default. First, it assumes the universe on x is a genome identifier and attempts to look up the corresponding metadata an installed BSgenome package or, if that fails, via UCSC. If that fails, it uses names(x) as the seqnames and end(range(x)) as the seqlengths.

Author(s)

Michael Lawrence