convert_sequence_to_numbers

This function takes a sequence and encodes it as a vector
of numbers for visualisation via <code>rasterise_matrix()</code>. 
Encoding: <code>A = 1</code>, <code>C = 2</code>, <code>G = 3</code>, <code>T/U = 4</code>.

Uses 'ggplot2' to visualise either (a) a single DNA/RNA sequence split across multiple lines, (b) multiple DNA/RNA sequences, each occupying a whole line, or (c) base modifications such as DNA methylation called by modified bases models in Dorado or Guppy. Functions starting with visualise_<something>() are the main plotting functions, and functions starting with extract_<something>() are key helper functions for reading files and reformatting data. Source code is available at <https://github.com/ejade42/ggDNAvis> and a full non-expert user guide is available at <https://ejade42.github.io/ggDNAvis/>.

Evelyn Jade

ggDNAvis

'ggplot2'-Based Tools for Visualising DNA Sequences and
Modifications

convert_sequence_to_numbers function

<dl><dt>sequence</dt>
<dd><code>character</code>. A DNA/RNA sequence (<code>A/C/G/T/U</code>) to be encoded numerically. No other characters allowed. Only one sequence allowed.</dd>
<dt>length</dt>
<dd><code>integer</code>. How long the output numerical vector should be. If shorter than the sequence, the vector will include the first n bases up to this length. If longer than the sequence, the vector will be padded with 0s at the end. If left blank/set to <code>NA</code> (default), will output a vector the same length as the input sequence.</dd></dl>

Arguments

This function takes a sequence and encodes it as a vector
of numbers for visualisation via <code>rasterise_matrix()</code>. 
Encoding: <code>A = 1</code>, <code>C = 2</code>, <code>G = 3</code>, <code>T/U = 4</code>.

Map a sequence to a vector of numbers (generic ggDNAvis helper) — convert_sequence_to_numbers

<dl>

<dt>sequence</dt>
<dd><code>character</code>. A DNA/RNA sequence (<code>A/C/G/T/U</code>) to be encoded numerically. No other characters allowed. Only one sequence allowed.</dd>


<dt>length</dt>
<dd><code>integer</code>. How long the output numerical vector should be. If shorter than the sequence, the vector will include the first n bases up to this length. If longer than the sequence, the vector will be padded with 0s at the end. If left blank/set to <code>NA</code> (default), will output a vector the same length as the input sequence.</dd>

</dl>

convert_sequence_to_numbers: Map a sequence to a vector of numbers (generic `ggDNAvis` helper)

Description

Usage

Value

Arguments

Examples