consensus-class

consensus

A toolkit for read and prepare immune repertoire data. 'TrustVDJ' package focuses on the reading and processing of 'TRUST4' and '10x cellranger' software output results by using 'ReadTrust' and 'Read10x' functions, respectively, and also provides a convenience function 'build_IMGT_reference' to download the 'IMGT' database reference and split its sequences by species.

Lianhao Song

TrustVDJ

Tools for Immune Repertoire Analysis

consensus-class function

<dl class="dl-horizontal">
<dt><code>Vgene</code></dt><dd>character. V gene, eg.: TRAV1*01</dd></dl><dt><code>Dgene</code></dt><dd>character. D gene, eg.: TRAD1*01</dd><dt><code>Jgene</code></dt><dd>character. J gene, eg.: TRAJ1*01</dd><dt><code>Cgene</code></dt><dd>character. C gene, eg.: TRAC1*01</dd><dt><code>CDR1dna</code></dt><dd>character. CDR1 nucleic acid sequence, eg.: TCTGAACACAACCGC</dd><dt><code>CDR2dna</code></dt><dd>character. CDR2 nucleic acid sequence, eg.: TTCCAGAATGAAGCTCAA</dd><dt><code>CDR3dna</code></dt><dd>character. CDR3 nucleic acid sequence, eg.: TGTGCCAGCAGCCTACGCAACGAGCAGTACTTC</dd><dt><code>CDR3aa</code></dt><dd>character. CDR3 amino acid sequence, eg.: CASSPTPGEATDTQYF</dd><dt><code>Count</code></dt><dd>numeric. Read counts, eg.: 200</dd><dt><code>ID</code></dt><dd>character. Consensus id, eg.: Sample1_consensus1</dd><dt><code>CDR3germlineSimilarity</code></dt><dd>numeric. CDR3 germline similarity score, eg.: 80</dd><dt><code>FullLength</code></dt><dd>logical. Whether the vdj gene is complete, eg.: TRUE</dd>

consensus-class: The consensus class

Description

Arguments

Value

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