XStringSet-class {Biostrings} | R Documentation |
The BStringSet class is a container for storing a set of BString
objects and for making its manipulation easy and efficient.
Similarly, the DNAStringSet (or RNAStringSet, or AAStringSet) class is
a container for storing a set of DNAString
(or RNAString
, or AAString
) objects.
The BStringList class (and family) is equivalent to the BStringSet family. It was a first attempt to address the problem of storing a large set of sequences but it has been superseded by the BStringSet family.
BStringSet(x, start=NA, end=NA, width=NA, use.names=TRUE) DNAStringSet(x, start=NA, end=NA, width=NA, use.names=TRUE) RNAStringSet(x, start=NA, end=NA, width=NA, use.names=TRUE) AAStringSet(x, start=NA, end=NA, width=NA, use.names=TRUE) ## The BStringList family has been superseded by the more efficient ## BStringSet family BStringList(x, start=NA, end=NA, width=NA, use.names=TRUE, check=TRUE) DNAStringList(x, start=NA, end=NA, width=NA, use.names=TRUE, check=TRUE) RNAStringList(x, start=NA, end=NA, width=NA, use.names=TRUE, check=TRUE) AAStringList(x, start=NA, end=NA, width=NA, use.names=TRUE, check=TRUE)
x |
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start |
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end |
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width |
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use.names |
[TODO] |
check |
[TODO] |
[TODO]
The XStringSet class derives from the IRanges class hence
all the accessor methods defined for a IRanges object can also
be used on an XStringSet object. In particular, the following methods
are available (in the code snippets below, x
is an XStringSet
object:
length(x)
:
The number of sequences in x
.
width(x)
:
A vector of non-negative integers containing the number
of letters for each element in x
.
nchar(x)
:
The same as width(x)
.
names(x)
:
NULL
or a character vector of the same length as x
containing
a short user-provided description or comment for each element in x
.
These are the only data in an XStringSet object that can safely
be changed by the user. All the other data are immutable!
As a general recommendation, the user should never try to modify
an object by accessing its slots directly.
In the code snippets below,
x
is an XStringSet object,
and i
should be an index specifying the elements to extract.
x[i]
:
Return a new XStringSet object made of the selected elements.
x[[i]]
:
Extract the i-th BString
object from x
.
In the code snippets below,
x
is an XStringSet object.
as.list(x)
:
Return the elements in x
as a standard R list.
H. Pages
BString-class, DNAString-class, RNAString-class, AAString-class, XStringViews-class, IRanges
x1 <- DNAStringSet(c("TTGA", "-CTC-N")) x1 names(x1) names(x1)[2] <- "seqB" x1 library(drosophila2probe) x2 <- DNAStringSet(drosophila2probe$sequence) x2 RNAStringSet(x2, start=2, end=-5)