BamViews {Rsamtools} | R Documentation

## 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

[Package Rsamtools version 2.10.0 Index]