fragments | R Documentation |
An R6 Class representing a fragments object.
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.
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()
.
new()
initialization function that is not used since the child classes are the main object of this package.
fragments$new(unique_id)
unique_id
unique_id
print()
A function to print informative information to the console
fragments$print()
plot_trace()
plot the trace data
fragments$plot_trace( show_peaks = TRUE, x_axis = NULL, ylim = NULL, xlim = NULL, signal_color_threshold = 0.05, plot_title = NULL )
show_peaks
A logical to say if the called peaks should be plotted on top of the trace. Only valid for fragments_repeats objects.
x_axis
Either "size" or "repeats" to indicate what should be plotted on the x-axis.
ylim
numeric vector length two specifying the y axis limits
xlim
numeric vector length two specifying the x axis limits
signal_color_threshold
A threshold value to colour the peaks relative to the tallest peak.
plot_title
A character string for setting the plot title. Defaults to the unique id of the object
A base R plot
clone()
The objects of this class are cloneable with this method.
fragments$clone(deep = FALSE)
deep
Whether to make a deep clone.
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