XStringSetList-class {Biostrings} | R Documentation |
The XStringSetList class is a virtual container for storing a list of XStringSet objects.
## Constructors: DNAStringSetList(..., 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()
is the only XStringSetList constructor.
The XStringSetList class itself is virtual and has no constructor.
In the code snippets below,
x
is an XStringSetList object.
length(x)
:
The number of list elements in x
.
PartitioningByEnd(x)
:
A PartitioningByEnd object describing the grouping
of the inner elements in x
within each top-level list element.
elementLengths(x)
:
An integer vector of the length of each list element of 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 XStringSetList
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
and values
are XStringSet objects,
and i
should be an index specifying the elements to extract.
x[[i]]
:
Extract the i-th XStringSet
object from x
.
append(x, values, after=length(x))
:
Add sequences in values
to x
.
H. Pages
XStringSet-class, Grouping-class, Vector-class
## ------------------------------------------------------------------------ ## A. THE XStringSetList CONSTRUCTORS ## ------------------------------------------------------------------------ ## Currently DNAStringSetList() is the only constructor. Others will ## be developed when the use case arises. dna1 <- DNAStringSet(c("AAA", "AC", "", "T", "GGATA")) dna2 <- DNAStringSet(c("G", "TT", "C")) x <- DNAStringSetList(dna1, dna2) x y <- DNAStringSetList(c("AAA", "AC", "", "T", "GGATA"), c("G", "TT", "C")) stopifnot(identical(x, y)) ## --------------------------------------------------------------------- ## B. UNLISTING AN XStringSetList OBJECT ## --------------------------------------------------------------------- length(x) elementLengths(x) unlist(x) x[[1]] x[[2]] as.list(x) names(x) <- LETTERS[1:length(x)] x[["A"]] x[["B"]] as.list(x) # named list ## --------------------------------------------------------------------- ## B. USING THE GROUPING CORE API ON 'PartitioningByEnd(x)' ## --------------------------------------------------------------------- PartitioningByEnd(x) length(PartitioningByEnd(x)) nobj(PartitioningByEnd(x)) grouplength(PartitioningByEnd(x)) # same as 'unname(sapply(x, length))' ## --------------------------------------------------------------------- ## C. USING THE RANGES CORE API ON 'PartitioningByEnd(x)' ## --------------------------------------------------------------------- start(PartitioningByEnd(x)) end(PartitioningByEnd(x)) width(PartitioningByEnd(x)) # same as 'grouplength(PartitioningByEnd(x))'