PileupFiles {Rsamtools} | R Documentation

## Represent BAM files for pileup summaries.

### Description

Use `PileupFiles()` to create a reference to BAM files (and their indicies), to be used for calculating pile-up summaries.

### Usage

    ## Constructors
    PileupFiles(files, ..., param=ApplyPileupsParam())
    ## S4 method for signature 'character'
    PileupFiles(files, ..., param=ApplyPileupsParam())
    ## S4 method for signature 'list'
    PileupFiles(files, ..., param=ApplyPileupsParam())

    ## opening / closing
    ## open(con, ...)
    ## close(con, ...)

    ## accessors; also path()
    ## S4 method for signature 'PileupFiles'
    isOpen(con, rw="")
    plpFiles(object)
    plpParam(object)

    ## actions
    ## S4 method for signature 'PileupFiles,missing'
    applyPileups(files, FUN, ..., param)
    ## S4 method for signature 'PileupFiles,ApplyPileupsParam'
    applyPileups(files, FUN, ..., param)

    ## display
    ## S4 method for signature 'PileupFiles'
    show(object)

### Arguments

`files` | For `PileupFiles`, a `character()` or `list` of `BamFile` instances representing files to be included in the pileup. Using a `list` of `BamFile` allows indicies to be specified when these are in non-standard format. All elements of `...` must be the same type. For `applyPileups,PileupFiles-method`, a `PileupFiles` instance.
`...` | Additional arguments, currently ignored.
`con, object` | An instance of `PileupFiles`.
`FUN` | A function of one argument; see `applyPileups`.
`param` | An instance of `ApplyPileupsParam`, to select which records to include in the pileup, and which summary information to return.
`rw` | character() indicating mode of file; not used for `TabixFile`.

### Objects from the Class

Objects are created by calls of the form `PileupFiles()`.

### Fields

The `PileupFiles` class is implemented as an S4 reference class. It has the following fields:

files

  A list of `BamFile` instances.

param

  An instance of `ApplyPileupsParam`.

### Functions and methods

Opening / closing:

open.PileupFiles

  Opens the (local or remote) `path` and `index` of each file in the `PileupFiles` instance. Returns a `PileupFiles` instance.

close.PileupFiles

  Closes each file in the `PileupFiles` instance; returning (invisibly) the updated `PileupFiles`. The instance may be re-opened with `open.PileupFiles`.

Accessors:

plpFiles

  Returns the `list` of the files in the `PileupFiles` instance.

plpParam

  Returns the `ApplyPileupsParam` content of the `PileupFiles` instance.

Methods:

applyPileups

  Calculate the pileup across all files in `files` according to criteria in `param` (or `plpParam(files)` if `param` is missing), invoking `FUN` on each range or collection of positions. See `applyPileups`.

show

  Compactly display the object.

### Author(s)

Martin Morgan

### Examples

    example(applyPileups)

[Package Rsamtools version 2.10.0 Index]