CHARGE_MUTATIONS

HYDROPATHY_MUTATIONS

MUTATION_SCHEMES

POLARITY_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

MUTATION_SCHEMES function

A <code><a rd-options="" href="/link/MutationDefinition?package=shazam&version=0.1.2" data-mini-rdoc="shazam::MutationDefinition">MutationDefinition</a></code> object defining:
<ul>
<li>  <code>CHARGE_MUTATIONS</code>:      Amino acid mutations are defined by changes
                                       in charge classes.
  </li>
<li>  <code>HYDROPATHY_MUTATIONS</code>:  Amino acid mutations are defined by changes
                                       in hydrophobicitity classes.
  </li>
<li>  <code>POLARITY_MUTATIONS</code>:    Amino acid mutations are defined by changes
                                       in polarity classes.
</li>
</ul>

MUTATION_SCHEMES: Amino acid mutation definitions

Description

Arguments

Format

References