MUTATION_SCHEMES

CHARGE_MUTATIONS

HYDROPATHY_MUTATIONS

POLARITY_MUTATIONS

VOLUME_MUTATIONS

Definitions of replacement (R) and silent (S) mutations for different amino acid
physicochemical classes.

Provides a computational framework for Bayesian estimation of
antigen-driven selection in immunoglobulin (Ig) sequences, providing an
intuitive means of analyzing selection by quantifying the degree of
selective pressure. Also provides tools to profile mutations in Ig
sequences, build models of somatic hypermutation (SHM) in Ig sequences,
and make model-dependent distance comparisons of Ig repertoires.

Jason Vander Heiden

shazam

Immunoglobulin Somatic Hypermutation Analysis

Mohamed Uduman

Gur Yaari

Namita Gupta

Ang Cui

Susanna Marquez

Julian Zhou

Nima Nouri

Steven Kleinstein

MUTATION_SCHEMES function

A <a rd-options="" href="/link/MutationDefinition?package=shazam&version=0.1.8" data-mini-rdoc="shazam::MutationDefinition">MutationDefinition</a> object defining:<ul>
<li><code>CHARGE_MUTATIONS</code>: Amino acid mutations are defined by changes
 in side chain charge class.</li>
<li><code>HYDROPATHY_MUTATIONS</code>: Amino acid mutations are defined by changes
 in side chain hydrophobicitity class.</li>
<li><code>POLARITY_MUTATIONS</code>: Amino acid mutations are defined by changes
 in side chain polarity class.</li>
<li><code>VOLUME_MUTATIONS</code>: Amino acid mutations are defined by changes
 in side chain volume class.</li>
</ul>

Format

Amino acid mutation definitions — MUTATION_SCHEMES

A <a rd-options='' href='MutationDefinition'>MutationDefinition</a> object defining:<ul>
<li><code>CHARGE_MUTATIONS</code>: Amino acid mutations are defined by changes
 in side chain charge class.</li>
<li><code>HYDROPATHY_MUTATIONS</code>: Amino acid mutations are defined by changes
 in side chain hydrophobicitity class.</li>
<li><code>POLARITY_MUTATIONS</code>: Amino acid mutations are defined by changes
 in side chain polarity class.</li>
<li><code>VOLUME_MUTATIONS</code>: Amino acid mutations are defined by changes
 in side chain volume class.</li>
</ul>

Amino acid mutation definitions

MUTATION_SCHEMES: Amino acid mutation definitions

Description

Arguments

Format

References