The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

trace 0.5.0

• 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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.