ChangeoClone-class

ChangeoClone

<code>ChangeoClone</code> defines a common data structure for perform lineage recontruction
from Change-O data.

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

Namita Gupta

Susanna Marquez

Nima Nouri

Ruoyi Jiang

Julian Zhou

Kenneth Hoehn

Daniel Gadala-Maria

Edel Aron

Steven Kleinstein

ChangeoClone-class function

<dl class="dl-horizontal">
<dt><code>data</code></dt><dd>data.frame containing sequences and annotations. Contains the
columns <code>SEQUENCE_ID</code> and <code>SEQUENCE</code>, as well as any additional 
sequence-specific annotation columns.</dd></dl><dt><code>clone</code></dt><dd>string defining the clone identifier.</dd><dt><code>germline</code></dt><dd>string containing the germline sequence for the clone.</dd><dt><code>v_gene</code></dt><dd>string defining the V segment gene call.</dd><dt><code>j_gene</code></dt><dd>string defining the J segment gene call.</dd><dt><code>junc_len</code></dt><dd>numeric junction length (nucleotide count).</dd>

Slots

S4 class defining a clone — ChangeoClone-class

S4 class defining a clone

ChangeoClone-class: S4 class defining a clone

Description

Arguments

Slots

See Also