ReferenceTrack-class {Gviz} | R Documentation

## ReferenceTrack class and methods

### Description

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

### Usage

    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.

### Value

Constructor functions of `AnnotationTrack`, `DataTrack`, `SequenceTrack` and `AlignmentsTrack` can create a special object of coresponding Reference*Track subclass with pointer to the referenced file.

### 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`

### Examples

    # This is a reference class, below example from AlignmentsTrack

    afrom <- 2960000
    ato <- 3160000
    alTrack <- AlignmentsTrack(system.file(package="Gviz", "extdata",
    "gapped.bam"), isPaired=TRUE)
    plotTracks(alTrack, from=afrom, to=ato, chromosome="chr12")

[Package Gviz version 1.34.1 Index]