XStringSetList-class {Biostrings} | R Documentation

## XStringSetList objects

### Description

The XStringSetList class is a virtual container for storing a list of XStringSet objects.

### Usage

    ## Constructors:
    BStringSetList(..., use.names=TRUE)
    DNAStringSetList(..., use.names=TRUE)
    RNAStringSetList(..., use.names=TRUE)
    AAStringSetList(..., use.names=TRUE)

### Arguments

`...` | Character vector(s) (with no NAs), or XStringSet object(s), or XStringViews object(s) to be concatenated into a XStringSetList.
`use.names` | `TRUE` or `FALSE`. Should names be preserved?

### Details

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.

### Methods

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.

### Author(s)

H. Pagès

### See Also

XStringSet-class, List-class

### Examples

    ## ------------------------------------------------------------------------
    ## 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 list

[Package Biostrings version 2.60.2 Index]