ReferenceTrack class and methods

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

availableDefaultMapping(file, trackType)

# S4 method for class 'ReferenceTrack'
initialize(
  .Object,
  stream,
  reference,
  mapping = list(),
  args = list(),
  defaults = list()
)

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.
.Object: The object skeleton passed on by new() during class instantiation, to be filled in by the initialize method.
stream: A function to stream the data from an indexed file. It has to accept the two arguments file and selection, and to return a GRanges object.
reference: A character scalar with the path to the referenced file.
mapping: A named list mapping the columns of the imported data to the metadata columns of the track's GRanges object.
args: A list of the arguments the object has been constructed with.
defaults: A list of the constructor's default arguments, used to fill in whatever has not been provided in args.

Value

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

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

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' GRanges objects.

Functions

availableDefaultMapping(): Function 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.
initialize(ReferenceTrack): Initialize all the ReferenceTrack slots (stream, reference, mapping, args, defaults) from the supplied arguments and validate the resulting object.

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.

Author

Florian Hahne

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")