Rsamtools: RsamtoolsFileList-class – R documentation

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RsamtoolsFileList-class

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

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