Changelog

trace 0.5.0

CRAN release: 2025-01-16

• expansion_ratio metric updated so that it starts at 1 rather than 0

  • It now includes the relative signal of the index peak in the metric

• find_fragments filters minimum_peak_signal on the raw signal rather than the smoothed signal

• extract_alleles now will always return allele_2 so that the column names are always consistent

trace 0.4.0

Along with a new name, this is a major update to the previous version of the package. The updates below are changes relative to the main branch of the ‘instability’ github branch.

Breaking changes

• Most main functions in the pipeline modify in place rather than return a new object for efficient use of memory

  • This applies to the following functions: find_ladders(), add_metadata(), find_alleles(), call_repeats(), and assign_index_peaks().

• Repeat correction changes

  • The argument repeat_length_correction has been removed from call_repeats() and been replaced with correction
  • Now you chose between “repeat” or “batch” correction (see call_repeats() documentation for more info)

• Metadata categories renamed

  • Renamed for clarity and to make it clearer which functionality it’s associated with
  • plate_id -> batch_id, group_id -> metrics_group_id
  • size_standard_repeat_length -> batch_sample_modal_repeat
  • “size_standard” removed due to unnecessary redundancy of category

• Renamed instability metrics for clarity:

  • average_repeat_gain to average_repeat_change
  • modal_repeat_delta to modal_repeat_change

• Renamed number_of_peaks_to_return to number_of_alleles in find_alleles()

• Allele and index peak information can no longer be directly interacted with in the class

  • Setters (fragment_repeats$set_allele_peak() & fragment_repeats$set_index_peak()) and getters (fragment_repeats$get_allele_peak() & fragment_repeats$get_index_peak()) have been introduced so users don’t accidentally break things if they chose to directly interact with objects.

• Removed backwards compatibility of index assignment in calculate_instability_metrics()

  • grouped and index_override_dataframe parameters removed from calculate_instability_metrics()

• Renamed spike_location parameter in find_ladders() to ladder_start_scan

• Removed fix_ladders_auto() function

• The function generate_instability_template() was renamed to generate_trace_template()

• fragment_trace class is now instantiated after read_fsa() function rather than find_ladders()

• Throughout the package renamed any mention of height to signal for consistency

New features

• Batch correction

  • Correct systematic batch effects that occur across fragment analysis runs by using common samples across runs without having to know the repeat length

  • New associated function plot_batch_correction_samples() to help visualize this batch correction

  • See documentation for call_repeats() for more info

• New instability metric instability_index_change

• New function extract_ladder_summary() to get a summary of the ladder fits for all samples

• New function plot_data_channels() to help identify the channels containing the ladder and raw data

Bug fixes

• If some samples do not having a metrics_group_id or metrics_baseline_control the calculate_instability_metrics() function will still run but those samples will have missing values