# Tandem Repeat Analysis by Capillary Electrophoresis

## Documentation for package ‘trace’ version 0.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

add_metadata | Add Metadata to Fragments List
assign_index_peaks | Assign index peaks
calculate_instability_metrics | Calculate Repeat Instability Metrics
call_repeats | Call Repeats for Fragments
cell_line_fsa_list | A list of fsa files
example_data | example_data
example_data_repeat_table | example_data_repeat_table
extract_alleles | Extract Modal Peaks
extract_fragments | Extract All Fragments
extract_ladder_summary | Extract ladder summary
extract_repeat_correction_summary | Extract repeat correction summary
extract_trace_table | Extract traces
find_alleles | Find Alleles
find_fragments | Find fragment peaks
find_ladders | Ladder and bp sizing
fix_ladders_interactive | Fix ladders interactively
fix_ladders_manual | Fix ladders manually
fragments | fragments object
fragments_repeats | fragments_repeats object
fragments_trace | fragments_trace object
generate_trace_template | Generate a Quarto file that has the instability pipeline preset
metadata | metadata
peak_table_to_fragments | Convert Peak Table to Fragments_repeats class
plot_batch_correction_samples | Plot correction samples
plot_data_channels | plot_data_channels
plot_fragments | Plot Peak Data
plot_ladders | Plot ladder
plot_repeat_correction_model | Plot Repeat Correction Model
plot_traces | Plot sample traces
read_fsa | Read fsa file
remove_fragments | Remove Samples from List
repeat_table_to_repeats | Convert Repeat Table to Repeats Fragments