convertNumbering

Converts numbering systems like Kabat or IMGT using these conventions:
http://www.imgt.org/IMGTScientificChart/Numbering/IMGT-Kabat_part1.html
with Gaps (unoccupied positions) shown by "G" and Asterisks (*) shown by "S": 
arbitrary mappings (multiple possible "to" values) represented with "NA"

Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.

Susanna Marquez

shazam

Immunoglobulin Somatic Hypermutation Analysis

Mohamed Uduman

Namita Gupta

Julian Zhou

Nima Nouri

Noah Yann Lee

Ang Cui

Jason Vander Heiden

Gur Yaari

Steven Kleinstein

convertNumbering function

<dl><dt>locus</dt>
<dd>string indicating heavy ("IGH") or light chains ("IGK" or "IGL)</dd>
<dt>from</dt>
<dd>string indicating numbering system to convert to ("IMGT" or "KABAT")</dd>
<dt>to</dt>
<dd>string indicating original numbering system ("IMGT" or "KABAT")</dd>
<dt>calls</dt>
<dd>vector of strings representing original numbering</dd></dl>

Arguments

convertNumbering: IMGT-Kabat number conversion — convertNumbering

<dl>

<dt>locus</dt>
<dd>string indicating heavy ("IGH") or light chains ("IGK" or "IGL)</dd>


<dt>from</dt>
<dd>string indicating numbering system to convert to ("IMGT" or "KABAT")</dd>


<dt>to</dt>
<dd>string indicating original numbering system ("IMGT" or "KABAT")</dd>


<dt>calls</dt>
<dd>vector of strings representing original numbering</dd>

</dl>

convertNumbering: IMGT-Kabat number conversion

convertNumbering: convertNumbering: IMGT-Kabat number conversion

Description

Usage

Value

Arguments

Examples