Package index • trace

Main functions

Process fsa files to generate instability metrics

read_fsa(): Read fsa file

add_metadata(): Add Metadata to Fragments List

find_ladders(): Ladder and bp sizing

find_fragments(): Find fragment peaks

find_alleles(): Find Alleles

call_repeats(): Call Repeats for Fragments

assign_index_peaks(): Assign index peaks

calculate_instability_metrics(): Calculate Repeat Instability Metrics

Plotting functions

Explore data through plots

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

Ladder fixing

Functions for fixing ladders

fix_ladders_interactive(): Fix ladders interactively

fix_ladders_manual(): Fix ladders manually

Helper functions

Useful functions for extracting information samples or modifying lists of objects

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

remove_fragments(): Remove Samples from List

Generate template

Functions that generate templates

generate_trace_template(): Generate a Quarto file that has the instability pipeline preset

Import data

Import data from non-fsa formats as a peak table or repeat table

peak_table_to_fragments(): Convert Peak Table to Fragments_repeats class

repeat_table_to_repeats(): Convert Repeat Table to Repeats Fragments

Package R6 objects

documentation for objects used in this package

fragments: fragments object

fragments_trace: fragments_trace object

fragments_repeats: fragments_repeats object

Example data

A collection of data that can be used for example analyses

cell_line_fsa_list: A list of fsa files

metadata: metadata

example_data: example_data

example_data_repeat_table: example_data_repeat_table