aliphatic

<code>aliphatic</code> calculates the aliphatic index of amino acid sequences using 
the method of Ikai. Non-informative positions are excluded, where non-informative 
is defined as any character in <code>c("X", "-", ".", "*")</code>.

Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.

Jason Vander Heiden

alakazam

Immunoglobulin Clonal Lineage and Diversity Analysis

Susanna Marquez

Namita Gupta

Nima Nouri

Ruoyi Jiang

Julian Zhou

Kenneth Hoehn

Daniel Gadala-Maria

Edel Aron

Steven Kleinstein

aliphatic function

<dl><dt>seq</dt>
<dd>vector of strings containing amino acid sequences.</dd>
<dt>normalize</dt>
<dd>if <code>TRUE</code> then divide the aliphatic index of each amino acid 
sequence by the number of informative positions. Non-informative 
position are defined by the presence any character in 
<code>c("X", "-", ".", "*")</code>. If <code>FALSE</code> then return the raw
aliphatic index.</dd></dl>

Arguments

Calculates the aliphatic index of amino acid sequences — aliphatic

<dl>

<dt>seq</dt>
<dd>vector of strings containing amino acid sequences.</dd>


<dt>normalize</dt>
<dd>if <code>TRUE</code> then divide the aliphatic index of each amino acid 
sequence by the number of informative positions. Non-informative 
position are defined by the presence any character in 
<code>c("X", "-", ".", "*")</code>. If <code>FALSE</code> then return the raw
aliphatic index.</dd>

</dl>

Calculates the aliphatic index of amino acid sequences

aliphatic: Calculates the aliphatic index of amino acid sequences

Description

Usage

Value

Arguments

References

Examples