Rsamtools: RsamtoolsFile-class – R documentation

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RsamtoolsFile-class

A base class for managing file references in Rsamtools

Description

RsamtoolsFile is a base class for managing file references in Rsamtools; it is not intended for direct use by users – see, e.g., BamFile.

Usage

## accessors
## S4 method for signature 'RsamtoolsFile'
path(object, ...)
## S4 method for signature 'RsamtoolsFile'
index(object, ..., asNA = TRUE)
## S4 method for signature 'RsamtoolsFile'
isOpen(con, rw="")
## S4 method for signature 'RsamtoolsFile'
yieldSize(object, ...)
yieldSize(object, ...) <- value
## S4 method for signature 'RsamtoolsFile'
show(object)

Arguments

`con, object`	An instance of a class derived from `RsamtoolsFile`.
`asNA`	logical indicating if missing output should be NA or character()
`rw`	Mode of file; ignored.
`...`	Additional arguments, unused.
`value`	Replacement value.

Objects from the Class

Users do not directly create instances of this class; see, e.g., BamFile-class.

Fields

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

.extptr: An externalptr initialized to an internal structure with opened bam file and bam index pointers.
path: A character(1) vector of the file name.
index: A character(1) vector of the index file name.
yieldSize: An integer(1) vector of the number of records to yield.

Functions and methods

Accessors:

path: Returns a character(1) vector of path names.
index: Returns a character(1) vector of index path names.
yieldSize, yieldSize<-: Return or set an integer(1) vector indicating yield size.

Methods:

isOpen: Report whether the file is currently open.
show: Compactly display the object.

Author(s)

Martin Morgan

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