XStringSetList objects
The XStringSetList class is a virtual container for storing a list of XStringSet objects.
## Constructors: BStringSetList(..., use.names=TRUE) DNAStringSetList(..., use.names=TRUE) RNAStringSetList(..., use.names=TRUE) AAStringSetList(..., use.names=TRUE)
... |
Character vector(s) (with no NAs), or XStringSet object(s), or XStringViews object(s) to be concatenated into a XStringSetList. |
use.names |
|
Concrete flavors of the XStringSetList container are the BStringSetList, DNAStringSetList, RNAStringSetList and AAStringSetList containers for storing a list of BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects, respectively. These four containers are direct subclasses of XStringSetList with no additional slots.
Currently DNAStringSetList() and AAStringSetList() are
the only XStringSetList constructors. The XStringSetList class itself
is virtual and has no constructor.
The XStringSetList class extends the List class defined
in the IRanges package. Using a less technical jargon, this just means
that an XStringSetList object is a list-like object that can be manipulated
like an ordinary list. Or, said otherwise, most of the operations that work
on an ordinary list (e.g. length, names, [, [[,
c, unlist, etc...) should work on an XStringSetList object.
In addition, Bioconductor specific list operations like
elementNROWS and
PartitioningByEnd (defined in the IRanges
package) are supported too.
H. Pagès
## ------------------------------------------------------------------------
## A. THE XStringSetList CONSTRUCTORS
## ------------------------------------------------------------------------
## Currently DNAStringSetList() and AAStringSetList() are the only
## constructors. Others will be developed when the use case arises.
dna1 <- c("AAA", "AC", "", "T", "GGATA")
dna2 <- c("G", "TT", "C")
x <- DNAStringSetList(dna1, dna2)
x
DNAStringSetList(DNAStringSet(dna1), DNAStringSet(dna2))
DNAStringSetList(dna1, DNAStringSet(dna2))
DNAStringSetList(DNAStringSet(dna1), dna2)
DNAStringSetList(dna1, RNAStringSet(DNAStringSet(dna2)))
DNAStringSetList(list(dna1, dna2))
DNAStringSetList(CharacterList(dna1, dna2))
## Empty object (i.e. zero-length):
DNAStringSetList()
## Not empty (length is 1):
DNAStringSetList(character(0))
## ---------------------------------------------------------------------
## B. UNLISTING AN XStringSetList OBJECT
## ---------------------------------------------------------------------
length(x)
elementNROWS(x)
unlist(x)
x[[1]]
x[[2]]
as.list(x)
names(x) <- LETTERS[1:length(x)]
x[["A"]]
x[["B"]]
as.list(x) # named listPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.