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