Package index • trace

Main functions

Process fsa files to generate instability metrics using these three functions

read_fsa(): Read fsa file
trace(): Main function for sample processing
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

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
load_config(): Load Trace Config File

Import data

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

genemapper_table_to_fragments(): Convert Genemapper Peak Table to fragments class
repeat_table_to_fragments(): Convert Repeat Table to Repeats Fragments
size_table_to_fragments(): Convert Size Table to Fragments

Package objects

documentation for objects used in this package

fragments: fragments 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