RangesList-methods {rtracklayer} | R Documentation |
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”).
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
.
Michael Lawrence