ReferenceTrack class and methods
A class allow for on-demand streaming of data off the file system.
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:
signature(.Object="ReferenceTrack"):
initialize the object.
Florian Hahne
# 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")
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