Rsamtools: BamViews-class – R documentation

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BamViews-class

Views into a set of BAM files

Description

Use BamViews() to reference a set of disk-based BAM files to be processed (e.g., queried using scanBam) as a single ‘experiment’.

Usage

## Constructor
BamViews(bamPaths=character(0),
     bamIndicies=bamPaths,
     bamSamples=DataFrame(row.names=make.unique(basename(bamPaths))),
     bamRanges, bamExperiment = list(), ...)
## S4 method for signature 'missing'
BamViews(bamPaths=character(0),
     bamIndicies=bamPaths,
     bamSamples=DataFrame(row.names=make.unique(basename(bamPaths))),
     bamRanges, bamExperiment = list(), ..., auto.range=FALSE)
## Accessors
bamPaths(x)
bamSamples(x)
bamSamples(x) <- value
bamRanges(x)
bamRanges(x) <- value
bamExperiment(x)

## S4 method for signature 'BamViews'
names(x)
## S4 replacement method for signature 'BamViews'
names(x) <- value
## S4 method for signature 'BamViews'
dimnames(x)
## S4 replacement method for signature 'BamViews,ANY'
dimnames(x) <- value

bamDirname(x, ...) <- value

## Subset
## S4 method for signature 'BamViews,ANY,ANY'
x[i, j, ..., drop=TRUE]
## S4 method for signature 'BamViews,ANY,missing'
x[i, j, ..., drop=TRUE]
## S4 method for signature 'BamViews,missing,ANY'
x[i, j, ..., drop=TRUE]

## Input
## S4 method for signature 'BamViews'
scanBam(file, index = file, ..., param = ScanBamParam(what=scanBamWhat()))
## S4 method for signature 'BamViews'
countBam(file, index = file, ..., param = ScanBamParam())

## Show
## S4 method for signature 'BamViews'
show(object)

Arguments

`bamPaths`	A character() vector of BAM path names.
`bamIndicies`	A character() vector of BAM index file path names, without the ‘.bai’ extension.
`bamSamples`	A `DataFrame` instance with as many rows as `length(bamPaths)`, containing sample information associated with each path.
`bamRanges`	Missing or a `GRanges` instance with ranges defined on the reference chromosomes of the BAM files. Ranges are not validated against the BAM files.
`bamExperiment`	A list() containing additional information about the experiment.
`auto.range`	If `TRUE` and all `bamPaths` exist, populate the ranges with the union of ranges returned in the `target` element of `scanBamHeader`.
`...`	Additional arguments.
`x`	An instance of `BamViews`.
`object`	An instance of `BamViews`.
`value`	An object of appropriate type to replace content.
`i`	During subsetting, a logical or numeric index into `bamRanges`.
`j`	During subsetting, a logical or numeric index into `bamSamples` and `bamPaths`.
`drop`	A logical(1), ignored by all `BamViews` subsetting methods.

`file`	An instance of `BamViews`.
`index`	A character vector of indices, corresponding to the `bamPaths(file)`.
`param`	An optional `ScanBamParam` instance to further influence scanning or counting.

Objects from the Class

Objects are created by calls of the form BamViews().

Slots

bamPaths: A character() vector of BAM path names.
bamIndicies: A character() vector of BAM index path names.
bamSamples: A DataFrame instance with as many rows as length(bamPaths), containing sample information associated with each path.
bamRanges: A GRanges instance with ranges defined on the spaces of the BAM files. Ranges are not validated against the BAM files.
bamExperiment: A list() containing additional information about the experiment.

Functions and methods

See 'Usage' for details on invocation.

Constructor:

BamViews:: Returns a BamViews object.

Accessors:

bamPaths: Returns a character() vector of BAM path names.
bamIndicies: Returns a character() vector of BAM index path names.
bamSamples: Returns a DataFrame instance with as many rows as length(bamPaths), containing sample information associated with each path.
bamSamples<-: Assign a DataFrame instance with as many rows as length(bamPaths), containing sample information associated with each path.
bamRanges: Returns a GRanges instance with ranges defined on the spaces of the BAM files. Ranges are not validated against the BAM files.
bamRanges<-: Assign a GRanges instance with ranges defined on the spaces of the BAM files. Ranges are not validated against the BAM files.
bamExperiment: Returns a list() containing additional information about the experiment.
names: Return the column names of the BamViews instance; same as names(bamSamples(x)).
names<-: Assign the column names of the BamViews instance.
dimnames: Return the row and column names of the BamViews instance.
dimnames<-: Assign the row and column names of the BamViews instance.

Methods:

"[": Subset the object by bamRanges or bamSamples.
scanBam: Visit each path in bamPaths(file), returning the result of scanBam applied to the specified path. bamRanges(file) takes precedence over bamWhich(param).
countBam: Visit each path in bamPaths(file), returning the result of countBam applied to the specified path. bamRanges(file) takes precedence over bamWhich(param).
show: Compactly display the object.

Author(s)

Martin Morgan

Examples

fls <- system.file("extdata", "ex1.bam", package="Rsamtools",
                   mustWork=TRUE)
rngs <- GRanges(seqnames = Rle(c("chr1", "chr2"), c(9, 9)),
                ranges = c(IRanges(seq(10000, 90000, 10000), width=500),
                           IRanges(seq(100000, 900000, 100000), width=5000)),
                Count = seq_len(18L))
v <- BamViews(fls, bamRanges=rngs)
v
v[1:5,]
bamRanges(v[c(1:5, 11:15),])
bamDirname(v) <- getwd()
v

Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

v2.6.0

Artistic-2.0 | file LICENSE

Authors

Martin Morgan, Hervé Pagès, Valerie Obenchain, Nathaniel Hayden

Initial release