repeat_table_to_fragments

This function converts a repeat table data frame into a list of fragments. class.

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>).

Zachariah McLean

trace

Tandem Repeat Analysis by Capillary Electrophoresis

Kevin Correia

Andrew Jiang

repeat_table_to_fragments function

<dl><dt>df</dt>
<dd>A data frame containing the repeat data with the columns "unique_id", "repeats", "signal".</dd>
<dt>min_repeat</dt>
<dd>minimum repeat size</dd>
<dt>max_repeat</dt>
<dd>maximum repeat size</dd></dl>

Arguments

Convert Repeat Table to Repeats Fragments — repeat_table_to_fragments

<dl>

<dt>df</dt>
<dd>A data frame containing the repeat data with the columns "unique_id", "repeats", "signal".</dd>


<dt>min_repeat</dt>
<dd>minimum repeat size</dd>


<dt>max_repeat</dt>
<dd>maximum repeat size</dd>

</dl>

repeat_table_to_fragments: Convert Repeat Table to Repeats Fragments

Description

Usage

Value

Arguments

Details

Examples