seqinfo {GenomicRanges} | R Documentation |
A set of generic functions for getting/setting sequence information from/on an object.
seqinfo(x) seqinfo(x, new2old=NULL) <- value seqnames(x) seqnames(x) <- value seqlevels(x) seqlevels(x) <- value seqlengths(x) seqlengths(x) <- value isCircular(x) isCircular(x) <- value isCircularWithKnownLength(x)
x |
The object from/on which to get/set the sequence information. |
new2old |
The new2old argument allows the user to rename, drop, add and/or
reorder the "sequence levels" in x .
If |
value |
Typically a Seqinfo object for the seqinfo setter.
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:
seqinfo
. That is, the seqnames
, seqlevels
,
seqlengths
, isCircular
and
isCircularWithKnownLength
getters are defined
for Seqinfo objects.
seqinfo
getter are typically
expected to return a Seqinfo object.
seqlevels
, seqlengths
, isCircular
and isCircularWithKnownLength
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))
,
and isCircularWithKnownLength(x)
does
isCircularWithKnownLength(seqinfo(x))
.
So any class with a seqinfo
getter that returns a
Seqinfo object also has all those getters working
out-of-the-box.
See the GRanges, GRangesList and GappedAlignments
classes as examples of such classes (those 3 classes are defined
in the GenomicRanges package).
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.
Seqinfo-class, GRanges-class, GRangesList-class, GappedAlignments-class
showMethods("seqinfo") showMethods("seqinfo<-") showMethods("seqnames") showMethods("seqnames<-") if (interactive()) ?`GRanges-class`