SnapshotFunction-class: Class "SnapshotFunction"

In ShortRead: FASTQ input and manipulation

Description

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

Usage

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

Arguments

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.

Fields

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.

Author(s)

Martin Morgan and Chao-Jen Wong

See Also

Snapshot

Examples

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

ShortRead documentation built on Nov. 8, 2020, 8:02 p.m.