Tandem Repeat Analysis by Capillary Electrophoresis
Add Metadata to Fragments List
Assign index peaks
Calculate Repeat Instability Metrics
Call Repeats for Fragments
Extract Modal Peaks
Extract All Fragments
Extract ladder summary
Extract repeat correction summary
Extract traces
Find Alleles
Find fragment peaks
Ladder and bp sizing
Fix ladders interactively
Fix ladders manually
fragments_repeats object
fragments_trace object
fragments object
Generate a Quarto file that has the instability pipeline preset
Convert Peak Table to Fragments_repeats class
Plot correction samples
plot_data_channels
Plot Peak Data
Plot ladder
Plot Repeat Correction Model
Plot sample traces
Read fsa file
Remove Samples from List
Convert Repeat Table to Repeats Fragments
trace: Tandem Repeat Analysis by Capillary Electrophoresis
A pipeline for short tandem repeat instability analysis from fragment analysis data. Inputs of fsa files or peak tables, and a user supplied metadata data-frame. The package identifies ladders, calls peaks, identifies the modal peaks, calls repeats, then calculates repeat instability metrics (e.g. expansion index from Lee et al. (2010) <doi:10.1186/1752-0509-4-29>).