RsamtoolsFileList {Rsamtools} | R Documentation

## A base class for managing lists of Rsamtools file references

### Description

`RsamtoolsFileList` is a base class for managing lists of file references in Rsamtools; it is not intended for direct use – see, e.g., `BamFileList`.

### Usage

    ## S4 method for signature 'RsamtoolsFileList'
    path(object, ...)
    ## S4 method for signature 'RsamtoolsFileList'
    index(object, ..., asNA = TRUE)
    ## S4 method for signature 'RsamtoolsFileList'
    isOpen(con, rw="")
    ## S3 method for class 'RsamtoolsFileList'
    open(con, ...)
    ## S3 method for class 'RsamtoolsFileList'
    close(con, ...)
    ## S4 method for signature 'RsamtoolsFileList'
    names(x)
    ## S4 method for signature 'RsamtoolsFileList'
    yieldSize(object, ...)

### Arguments

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

### Objects from the Class

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

### Functions and methods

This class inherits functions and methods for subseting, updating, and display from the `SimpleList` class.

Methods:

isOpen:

  Report whether each file in the list is currently open.

open:

  Attempt to open each file in the list.

close:

  Attempt to close each file in the list.

names:

  Names of each element of the list or, if names are `NULL`, the basename of the path of each element.

### Author(s)

Martin Morgan

[Package Rsamtools version 2.2.3 Index]