calculate_instability_metrics() with
missing index samplesexpansion_ratio metric updated so that it starts at
1 rather than 0
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
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.
Most main functions in the pipeline modify in place rather than return a new object for efficient use of memory
find_ladders(), add_metadata(),
find_alleles(), call_repeats(), and
assign_index_peaks().Repeat correction changes
repeat_length_correction has been removed
from call_repeats() and been replaced with
correctioncall_repeats() documentation for more info)Metadata categories renamed
Renamed instability metrics for clarity:
average_repeat_gain to
average_repeat_changemodal_repeat_delta to
modal_repeat_changeRenamed 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
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
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