ReferenceTrack-class: ReferenceTrack class and methods
In Gviz: Plotting data and annotation information along genomic coordinates

Description Usage Arguments Details Value Objects from the class Slots Methods Author(s) See Also Examples

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

1	availableDefaultMapping(file, trackType)

`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.

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.

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

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

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.

Internal methods:

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

Florian Hahne

GRanges

IRanges

# 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")