BSgenomeViews-class {BSgenome} | R Documentation

## BSgenomeViews objects

### Description

The BSgenomeViews class is a container for storing a set of genomic positions on a BSgenome object, called the "subject" in this context.

### Usage

    ## Constructor
    ## ------------

    BSgenomeViews(subject, granges)

    ## Accessors
    ## ---------

    ## S4 method for signature 'BSgenomeViews'
    subject(x)
    ## S4 method for signature 'BSgenomeViews'
    granges(x, use.mcols=FALSE)

    ## S4 method for signature 'BSgenomeViews'
    length(x)
    ## S4 method for signature 'BSgenomeViews'
    names(x)
    ## S4 method for signature 'BSgenomeViews'
    seqnames(x)
    ## S4 method for signature 'BSgenomeViews'
    start(x)
    ## S4 method for signature 'BSgenomeViews'
    end(x)
    ## S4 method for signature 'BSgenomeViews'
    width(x)
    ## S4 method for signature 'BSgenomeViews'
    strand(x)
    ## S4 method for signature 'BSgenomeViews'
    ranges(x, use.mcols=FALSE)
    ## S4 method for signature 'BSgenomeViews'
    elementNROWS(x)
    ## S4 method for signature 'BSgenomeViews'
    seqinfo(x)

    ## DNAStringSet methods
    ## --------------------

    ## S4 method for signature 'BSgenomeViews'
    seqtype(x)

    ## S4 method for signature 'BSgenomeViews'
    nchar(x, type="chars", allowNA=FALSE)

    ## S4 method for signature 'BSgenomeViews'
    unlist(x, recursive=TRUE, use.names=TRUE)

    ## S4 method for signature 'BSgenomeViews'
    alphabetFrequency(x, as.prob=FALSE, collapse=FALSE, baseOnly=FALSE)

    ## S4 method for signature 'BSgenomeViews'
    hasOnlyBaseLetters(x)

    ## S4 method for signature 'BSgenomeViews'
    uniqueLetters(x)

    ## S4 method for signature 'BSgenomeViews'
    letterFrequency(x, letters, OR="|", as.prob=FALSE, collapse=FALSE)

    ## S4 method for signature 'BSgenomeViews'
    oligonucleotideFrequency(x, width, step=1,
                             as.prob=FALSE, as.array=FALSE,
                             fast.moving.side="right", with.labels=TRUE, simplify.as="matrix")

    ## S4 method for signature 'BSgenomeViews'
    nucleotideFrequencyAt(x, at, as.prob=FALSE, as.array=TRUE,
                          fast.moving.side="right", with.labels=TRUE)

    ## S4 method for signature 'BSgenomeViews'
    consensusMatrix(x, as.prob=FALSE, shift=0L, width=NULL, baseOnly=FALSE)

    ## S4 method for signature 'BSgenomeViews'
    consensusString(x, ambiguityMap=IUPAC_CODE_MAP, threshold=0.25,
                    shift=0L, width=NULL)

### Arguments

`subject` | A BSgenome object or the name of a reference genome specified in a way that is accepted by the `getBSgenome` function. In that case the corresponding BSgenome data package needs to be already installed (see `?getBSgenome` for the details).
`granges` | A GRanges object containing ranges relative to the genomic sequences stored in `subject`.
`x` | A BSgenomeViews object.
`use.mcols` | `TRUE` or `FALSE` (the default). Whether the metadata columns on `x` (accessible with `mcols(x)`) should be propagated to the returned object or not.
`type, allowNA, recursive, use.names` | Ignored.
`as.prob, letters, OR, width` | See `?alphabetFrequency` and `?oligonucleotideFrequency` in the Biostrings package.
`collapse, baseOnly` | See `?alphabetFrequency` in the Biostrings package.
`step, as.array, fast.moving.side, with.labels, simplify.as, at` | See `?oligonucleotideFrequency` in the Biostrings package.
`shift, ambiguityMap, threshold` | See `?consensusMatrix` in the Biostrings package.

### Constructors

  `BSgenomeViews(subject, granges)`: Make a BSgenomeViews object by putting the views specified by `granges` on top of the genomic sequences stored in `subject`. See above for how argument `subject` and `granges` should be specified.

  `Views(subject, granges)`: Equivalent to `BSgenomeViews(subject, granges)`. Provided for convenience.

### Accessors

In the code snippets below, `x` is a BSgenomeViews object.

  `subject(x)`: Return the BSgenome object containing the full genomic sequences on top of which the views in `x` are defined.

  `granges(x, use.mcols=FALSE)`: Return the genomic ranges of the views as a GRanges object. These ranges are relative to the genomic sequences stored in `subject(x)`.

  `length(x)`: The number of views in `x`.

  `names(x)`: The names of the views in `x`.

  `seqnames(x)`, `start(x)`, `end(x)`, `width(x)`, `strand(x)`: Equivalent to `seqnames(granges(x))`, `start(granges(x))`, `end(granges(x))`, `width(granges(x))`, `strand(granges(x))`, respectively.

  `ranges(x, use.mcols=FALSE)`: Equivalent to `ranges(granges(x, use.mcols), use.mcols)`.

  `elementNROWS(x)`: Equivalent to `width(x)`.

  `seqinfo(x)`: Equivalent to `seqinfo(subject(x))` and to `seqinfo(granges(x))` (both are guaranteed to be the same). See `?seqinfo` in the GenomeInfoDb package for more information.

### Coercion

In the code snippets below, `x` is a BSgenomeViews object.

  `as(x, "DNAStringSet")`: Turn `x` into a DNAStringSet object by extxracting the DNA sequence corresponding to each view. Alternatively `as(x, "XStringSet")` can be used for this, and is equivalent to `as(x, "DNAStringSet")`.

  `as.character(x)`: Equivalent to `as.character(as(x, "DNAStringSet"))`.

  `as.data.frame(x)`: Turn `x` into a data.frame.

### Subsetting

  `x[i]`: Select the views specified by `i`.

  `x[[i]]`: Extract the one view specified by `i`.

### DNAStringSet methods

For convenience, some methods defined for DNAStringSet objects in the Biostrings package can be used directly on a BSgenomeViews object. In that case, everything happens like if the BSgenomeViews object `x` was turned into a DNAStringSet object (with `as(x, "DNAStringSet")`) before it's passed to the method for DNAStringSet objects.

At the moment, the list of such methods is: `seqtype`, `nchar,XStringSet-method`, `unlist,XStringSet-method`, `alphabetFrequency`, `hasOnlyBaseLetters`, `uniqueLetters`, `letterFrequency`, `oligonucleotideFrequency`, `nucleotideFrequencyAt`, `consensusMatrix`, and `consensusString`.

See the corresponding man page in the Biostrings package for a description of these methods.

### Author(s)

H. Pagès

### See Also

- The BSgenome class.

- The GRanges class in the GenomicRanges package.

- The DNAStringSet class in the Biostrings package.

- The seqinfo and related getters in the GenomeInfoDb package for getting the sequence information stored in an object.

- TxDb objects in the GenomicFeatures package.

### Examples

    library(BSgenome.Mmusculus.UCSC.mm10)
    genome <- BSgenome.Mmusculus.UCSC.mm10
    library(TxDb.Mmusculus.UCSC.mm10.knownGene)
    txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
    ex <- exons(txdb, columns=c("exon_id", "tx_name", "gene_id"))
    v <- Views(genome, ex)
    v

    subject(v)
    granges(v)
    seqinfo(v)
    as(v, "DNAStringSet")

    v10 <- v[1:10]  # select the first 10 views
    subject(v10)    # same as subject(v)
    granges(v10)
    seqinfo(v10)    # same as seqinfo(v)
    as(v10, "DNAStringSet")
    alphabetFrequency(v10)
    alphabetFrequency(v10, collapse=TRUE)

    v12 <- v[width(v) <= 12]  # select the views of 12 nucleotides or less
    head(as.data.frame(v12))
    trinucleotideFrequency(v12, simplify.as="collapsed")

    ## BSgenomeViews objects are list-like objects. That is, the
    ## BSgenomeViews class derives from List and typical list/List
    ## operations (e.g. [[, elementNROWS(), unlist(), elementType(),
    ## etc...) work on these objects:
    is(v12, "List")  # TRUE
    v12[[2]]
    head(elementNROWS(v12))  # elementNROWS(v) is the same as width(v)
    unlist(v12)
    elementType(v12)

[Package BSgenome version 1.50.0 Index]