Rsamtools: PileupFiles-class – R documentation

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PileupFiles-class

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)

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