BSgenome: BSgenomeViews-class – R documentation

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BSgenomeViews-class

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

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)

BSgenome

Software infrastructure for efficient representation of full genomes and their SNPs

v1.58.0

Artistic-2.0

Authors

Hervé Pagès

Initial release