repeat_table_to_repeats

This function converts a repeat table data frame into a list of fragments_repeats. 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_repeats function

<dl><dt>df</dt>
<dd>A data frame containing the repeat data.</dd>
<dt>unique_id</dt>
<dd>A character string indicating the column name for unique identifiers.</dd>
<dt>repeat_col</dt>
<dd>A character string indicating the column name for the repeats.</dd>
<dt>frequency_col</dt>
<dd>A character string indicating the column name for the repeat frequencies.</dd></dl>

Arguments

Convert Repeat Table to Repeats Fragments — repeat_table_to_repeats

<dl>

<dt>df</dt>
<dd>A data frame containing the repeat data.</dd>


<dt>unique_id</dt>
<dd>A character string indicating the column name for unique identifiers.</dd>


<dt>repeat_col</dt>
<dd>A character string indicating the column name for the repeats.</dd>


<dt>frequency_col</dt>
<dd>A character string indicating the column name for the repeat frequencies.</dd>

</dl>

repeat_table_to_repeats: Convert Repeat Table to Repeats Fragments

Description

Usage

Value

Arguments

Details

Examples