seqinfo {GenomicRanges} | R Documentation |
A set of generic functions for getting/setting sequence information from/on an object.
seqinfo(x) seqinfo(x, new2old=NULL, force=FALSE) <- value seqnames(x) seqnames(x) <- value seqlevels(x) seqlevels(x, force=FALSE) <- value seqlengths(x) seqlengths(x) <- value isCircular(x) isCircular(x) <- value genome(x) genome(x) <- value seqnameStyle(x) seqnameStyle(x) <- value
x |
The object from/on which to get/set the sequence information. |
new2old |
The
If |
force |
Force dropping sequence levels currently in use. This is achieved by
dropping the elements in |
value |
Typically a Seqinfo object for the Either a named or unnamed character vector for the A vector containing the sequence information to store for the other setters. |
Various classes implement methods for those generic functions.
The Seqinfo class plays a central role for those generics because:
It has methods for all those generics (except seqinfo
).
That is, the seqnames
, seqlevels
, seqlengths
,
isCircular
, genome
and seqnameStyle
getters
and setters are defined for Seqinfo objects.
For classes that implement it, the seqinfo
getter should
return a Seqinfo object.
Default seqlevels
, seqlengths
, isCircular
,
genome
, and seqnameStyle
getters and setters are
provided.
By default, seqlevels(x)
does seqlevels(seqinfo(x))
,
seqlengths(x)
does seqlengths(seqinfo(x))
,
isCircular(x)
does isCircular(seqinfo(x))
,
genome(x)
does genome(seqinfo(x))
,
and seqnameStyle(x)
does seqnameStyle(seqinfo(x))
.
So any class with a seqinfo
getter will have all the above
getters work out-of-the-box. If, in addition, the class defines
a seqinfo
setter, then all the corresponding setters will
also work out-of-the-box.
See the GRanges, GRangesList, GappedAlignments,
and GappedAlignmentPairs classes for examples of classes that
define the seqinfo
getter and setter (those 4 classes are
defined in the GenomicRanges package).
See the TranscriptDb class (defined in the
GenomicFeatures package) for an example of a class that defines only
the seqinfo
getter (no setter).
The GenomicRanges package defines seqinfo
and
seqinfo<-
methods for these low-level IRanges data
structures: List
, RangesList
and
RangedData
. Those objects do not have the means to formally
store sequence information. Thus, the wrappers simply store the
Seqinfo
object within metadata(x)
. Initially, the
metadata is empty, so there is some effort to generate a
reasonable default Seqinfo
. The names of any List
are taken as the seqnames
, and the universe
of
RangesList
or RangedData
is taken as the
genome
.
The full list of methods defined for a given generic can
be seen with e.g. showMethods("seqinfo")
or
showMethods("seqnames")
(for the getters),
and showMethods("seqinfo<-")
or showMethods("seqnames<-")
(for the setters aka replacement methods).
Please be aware that this shows only methods defined in packages
that are currently attached.
showMethods("seqinfo") showMethods("seqinfo<-") showMethods("seqnames") showMethods("seqnames<-") if (interactive()) ?`GRanges-class`