Skip to contents

fragments object

fragments.Rd

An R6 Class representing a fragments object.

Details

This is the parent class of both fragments_trace and fragments_repeats object. The idea is that shared fields and methods are both inherited from this object, but it is not itself directly used.

Public fields

unique_id

unique id of the sample usually the file name

metrics_group_id

sample grouping for metrics calculations. Associated with add_metadata().

metrics_baseline_control

logical to indicate if sample is the baseline control. Associated with add_metadata().

batch_run_id

fragment analysis run. Associated with add_metadata().

batch_sample_id

An id for the sample used as size standard for repeat calculation. Associated with add_metadata().

batch_sample_modal_repeat

Validated repeat length for the modal repeat repeat in that sample. Associated with add_metadata().

Methods

Public methods

Method new()

initialization function that is not used since the child classes are the main object of this package.

Usage

fragments$new(unique_id)

Arguments

unique_id

unique_id

Method print()

A function to print informative information to the console

Usage

fragments$print()

Method plot_trace()

plot the trace data

Usage

fragments$plot_trace(
  show_peaks = TRUE,
  x_axis = NULL,
  ylim = NULL,
  xlim = NULL,
  signal_color_threshold = 0.05,
  plot_title = NULL
)

Arguments

show_peaks

A logical to say if the called peaks should be plotted on top of the trace. Only valid for fragments_repeats objects.

x_axis

Either "size" or "repeats" to indicate what should be plotted on the x-axis.

ylim

numeric vector length two specifying the y axis limits

xlim

numeric vector length two specifying the x axis limits

signal_color_threshold

A threshold value to colour the peaks relative to the tallest peak.

plot_title

A character string for setting the plot title. Defaults to the unique id of the object

Returns

A base R plot

Method clone()

The objects of this class are cloneable with this method.

Usage

fragments$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.