fragments object

An R6 Class representing a fragments object.

Details

This is the parent class of both fragments and fragments 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

input_method

pathway used to import data (either 'fsa', 'size', or 'repeats')

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().

fsa

The whole fsa file, output from seqinr::read.abif()

raw_ladder

The raw data from the ladder channel

raw_data

The raw data from the sample channel

scan

The scan number

off_scale_scans

vector indicating which scales were too big and off scale. Note can be in any channel

ladder_df

A dataframe of the identified ladder from find_ladders(). Scan is the scan number of peak and size is the associated bp size.

ladder_total_combinations_tested

A numeric value indicating how many total combinations were tested during ladder fit

trace_bp_df

A dataframe of bp size for every scan from find_ladders().

peak_table_df

A dataframe containing the fragment peak level information.

repeat_table_df

A dataframe containing the fragment peak level information with the repeat size added. May or may not be the same as peak_table_df depending on what options are chosen in call_repeats.

Methods

Public methods

• fragments$new()

• fragments$print()

• fragments$plot_trace()

• fragments$plot_ladder()

• fragments$plot_data_channels()

• fragments$get_allele_peak()

• fragments$set_allele_peak()

• fragments$get_index_peak()

• fragments$set_index_peak()

• fragments$plot_fragments()

• fragments$clone()

---

Method new()

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

Usage

fragments$new(unique_id, input_method, object)

Arguments

unique_id

unique_id

input_method

pathway used to import data (either 'fsa', 'size', or 'repeats')

object

object to be inserted into either 'fsa', 'peak_table_df', or 'repeat_table_df'

---

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 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 plot_ladder()

plot the ladder data

Usage

fragments$plot_ladder(xlim = NULL, ylim = NULL, plot_title = NULL)

Arguments

xlim

numeric vector length two specifying the x axis limits

ylim

numeric vector length two specifying the y axis limits

plot_title

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

Returns

A base R plot

---

Method plot_data_channels()

plot the raw data channels in the fsa file. It identifies every channel that has "DATA" in its name.

Usage

fragments$plot_data_channels()

Returns

A base R plot

---

Method get_allele_peak()

This returns a list with the allele information for this object.

Usage

fragments$get_allele_peak()

---

Method set_allele_peak()

This sets a single allele size/repeat. It searches through the appropriate peak table and finds the closest peak to the value that's provided.

Usage

fragments$set_allele_peak(allele, unit, value)

Arguments

allele

Either 1 or 2, indicating which allele information should be set. Allele 1 is the only one used for repeat instability metrics calculations.

unit

Either "size" or "repeats" to indicate if the value you're providing is bp size or repeat length.

value

Numeric vector (length one) of the size/repeat length to set.

---

Method get_index_peak()

This returns a list with the index peak information for this object.

Usage

fragments$get_index_peak()

---

Method set_index_peak()

This sets the index repeat length. It searches through the repeat table and finds the closest peak to the value that's provided.

Usage

fragments$set_index_peak(value)

Arguments

value

Numeric vector (length one) of the repeat length to set as index peak.

---

Method plot_fragments()

This plots the peak/repeat table as a histogram

Usage

fragments$plot_fragments(ylim = NULL, xlim = NULL, plot_title = NULL)

Arguments

ylim

numeric vector length two specifying the y axis limits

xlim

numeric vector length two specifying the x axis limits

plot_title

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

---

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.