RTLFile-class: RTLFile objects

In rtracklayer: R interface to genome annotation files and the UCSC genome browser

Description

A RTLFile object is the base class for classes representing files accessible with rtracklayer. It wraps a resource (either a path, URL or connection). We can represent a list of RTLFile objects with a RTLFileList.

Accessor Methods

In the code snippets below, x represents a RTLFile object.

path(x): Gets the path, as a character vector, to the resource represented by the RTLFile object, if possible.

resource(x): Gets the low-level resource, either a character vector (a path or URL) or a connection.

fileFormat(x): Gets a string identifying the file format. Can also be called directly on a character file path, in which case it uses a heuristic based on the file extension.

Coercion

as.character(x): Returns the path of the file as a character vector.

Related functions

FileForFormat(path, format = file_ext(path)): Determines the file type of path and returns a high-level file object such as BamFile, BEDFile, BigWigFile etc..

Author(s)

Michael Lawrence

See Also

Implementing classes include: BigWigFile, TwoBitFile, BEDFile, GFFFile, and WIGFile.

rtracklayer documentation built on Nov. 8, 2020, 6:50 p.m.