RsamtoolsFile {Rsamtools} | R Documentation

## 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

[Package Rsamtools version 1.32.3 Index]