Tandem Repeat Analysis by Capillary Electrophoresis


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Documentation for package ‘trace’ version 0.6.0

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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