| 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 It was a first attempt to address the problem of storing a large set of sequences but it has been superseded by the BStringSet family.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width=NA, use.names=TRUE) AAStringSet(x, start=NA, end=NA, width=NA, use.names=TRUE) ## The BStringList family has been superseded by the more efficient ## BStringSet family BStringList(x, start=NA, end=NA, width=NA, use.names=TRUE, check=TRUE) DNAStringList(x, start=NA, end=NA, width=NA,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 |
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check |
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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)