read.sanger

This function parses a FSA/AB1 file using <code>read.fsa</code>, with few adjustments for Sanger sequencing experiments.

A flexible and interfaced framework for importing, processing and ploting Applied Biosystems data files. Application to Reverse-Transcriptase Multiplex Ligation-dependent Probe Amplification (RT-MLPA) gene-expression profiling and classification is illustrated in Mareschal, Ruminy et al (2015) <doi:10.1016/j.jmoldx.2015.01.007>. Gene-fusion detection and Sanger sequencing are illustrated in Mareschal, Palau et al (2021) <doi:10.1182/bloodadvances.2020002517>. Examples are provided for genotyping applications as well.

Sylvain Mareschal

FSAtools

Fragment Analysis and Capillary Sequencing Tool Kit

Philippe Ruminy

Fabrice Jardin

read.sanger function

<dl> <dt>file</dt>
<dd>Single character value, the name and path of the file to parse.</dd> <dt>channelOrder</dt>
<dd>Character vector, providing 'A', 'C', 'G' and 'T' in the order of the used channels. If <code>NULL</code>, a guess will be attempted based on the called sequence.</dd> <dt>guess.threshold</dt>
<dd>Single numeric value, setting the tolerance to use for channel guessing validation. Lower values mean higher chances to get an error for channel guessing failure.</dd> <dt>processed</dt>
<dd>To be passed to <code>read.fsa</code>.</dd> <dt>lowess</dt>
<dd>To be passed to <code>read.fsa</code>.</dd> <dt>...</dt>
<dd>To be passed to <code>read.fsa</code>.</dd></dl>

Arguments

Author

Imports a .ab1 file from Applied Biosystems corresponding to Sanger sequencing — read.sanger

<dl>

 <dt>file</dt>
<dd>Single character value, the name and path of the file to parse.</dd>

 <dt>channelOrder</dt>
<dd>Character vector, providing 'A', 'C', 'G' and 'T' in the order of the used channels. If <code>NULL</code>, a guess will be attempted based on the called sequence.</dd>

 <dt>guess.threshold</dt>
<dd>Single numeric value, setting the tolerance to use for channel guessing validation. Lower values mean higher chances to get an error for channel guessing failure.</dd>

 <dt>processed</dt>
<dd>To be passed to <code>read.fsa</code>.</dd>

 <dt>lowess</dt>
<dd>To be passed to <code>read.fsa</code>.</dd>

 <dt>...</dt>
<dd>To be passed to <code>read.fsa</code>.</dd>

</dl>

read.sanger: Imports a .ab1 file from Applied Biosystems corresponding to Sanger sequencing

Description

Usage

Value

Arguments

Author

See Also