ReferenceTrack class and methods

Description

A class allow for on-demand streaming of data off the file system.

Usage

1
availableDefaultMapping(file, trackType)

Arguments

file

A character scalar with a file name or just a file extension.

trackType

A character scalar with one of the available track types in the package.

Details

The availableDefaultMappings function can be used to find out whether the package defines a mapping scheme between one of the many supported input file types and the metadata columns of the tracks's GRanges objects.

Objects from the class

A virtual class: No objects may be created from it.

Slots

stream:

Object of class function. The import function to stream data of the file system. Needs to be able to handle the two mandatory arguments file (a character containing a valid file path) and selection (a GRanges object with the genomic region to plot).

reference:

Object of class "character", the path to the file containing the data.

mapping:

Object of class "list", a default mapping between the metadata columns of the returned GRanges object from the import function and the elemenMetadata columns that make up the final track object.

args:

Object of class "list", the passed in constructor arguments during object instantiation. Those will be needed when fetching the data in order to fill all necessary slots.

defaults:

Object of class "list", the relevant default values to be used when neither mapping nor args provides the necessary information.

Methods

Internal methods:

initialize

signature(.Object="ReferenceTrack"): initialize the object.

Author(s)

Florian Hahne

See Also

AnnotationTrack

DisplayPars

GdObject

GeneRegionTrack

GRanges

ImageMap

IRanges

RangeTrack

DataTrack

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