ShortRead: SnapshotFunction-class – R documentation

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SnapshotFunction-class

Class "SnapshotFunction"

A class to store custom reader and viewer functions for the Snapshot class.

SnapshotFunction(reader, viewer, limits, ...)
reader(x, ...)
viewer(x, ...)
limits(x, ...)

`reader`	A function for reading data. The function must take a single argument (a `Snapshot` instance) and return a `data.frame` summarizing the file.
`viewer`	A function for visualizing the data. The function must accept the `data.frame` created by `reader`, and return an `SpTrellis` object representing the view.
`limits`	An integer(2) indicating the minimum and maximum number of nucleotides the `SnapshotFunction` is intended to visualize. For instance, a ‘fine-scale’ viewer displaying a pileup might be appropriate at between 1000 and 50000 nucleotides.
`x`	An instance of `SnapshotFunction`
`...`	Additional arguments, currently unused.

reader:: Object of class function for reading data from BAM files and returning a data.frame.
viewer:: Object of class function for visualization that returns an SpTrellis object.
limits:: Object of class integer for the limits of ranges to be visualized.

Martin Morgan and Chao-Jen Wong

## internally defined function
reader(ShortRead:::.fine_coverage)
viewer(ShortRead:::.fine_coverage)
limits(ShortRead:::.fine_coverage)

FASTQ input and manipulation

v1.48.0

Artistic-2.0

Authors

Martin Morgan, Michael Lawrence, Simon Anders

Initial release