freq_eval

The output of <code><a rd-options="" href="/link/freq_estimate?package=alphabetr&version=0.2.2" data-mini-rdoc="alphabetr::freq_estimate">freq_estimate</a></code>

freq

The number of clones represent the top proportion of
the T cell population by frequency (this is the same <code>number_skewed</code>
argument used when <code><a rd-options="" href="/link/create_clones?package=alphabetr&version=0.2.2" data-mini-rdoc="alphabetr::create_clones">create_clones</a></code> is called)

number_skewed

The clonal structure of the simulated T cell population. This is
obtained by subsetting the <code>TCR</code> element of the output of
<code><a rd-options="" href="/link/create_clones?package=alphabetr&version=0.2.2" data-mini-rdoc="alphabetr::create_clones">create_clones</a></code>

Total number of distinct clones in the parent population

numb_clones

The proportion of the population in frequency represented by
the number of clones specified by <code>skewed</code>.

prop_top


<code>freq_eval()</code> will evaluated how well <code><a rd-options="" href="/link/freq_estimate?package=alphabetr&version=0.2.2" data-mini-rdoc="alphabetr::freq_estimate">freq_estimate</a></code> performed
by calculating the precision and CV of the frequency estimates for the top
clones and by determining the proportion of the top clones whose true clonal
frequency lies in the 95-percent CI determined by <code><a rd-options="" href="/link/freq_estimate?package=alphabetr&version=0.2.2" data-mini-rdoc="alphabetr::freq_estimate">freq_estimate</a></code>


Provides algorithms for frequency-based pairing of alpha-beta T
cell receptors.

Edward Lee

alphabetr

Algorithms for High-Throughput Sequencing of Antigen-Specific T
Cells

freq_eval function

The output of <code><a rd-options='' href='freq_estimate'>freq_estimate</a></code>

The number of clones represent the top proportion of
the T cell population by frequency (this is the same <code>number_skewed</code>
argument used when <code><a rd-options='' href='create_clones'>create_clones</a></code> is called)

The clonal structure of the simulated T cell population. This is
obtained by subsetting the <code>TCR</code> element of the output of
<code><a rd-options='' href='create_clones'>create_clones</a></code>


<code>freq_eval()</code> will evaluated how well <code><a rd-options='' href='freq_estimate'>freq_estimate</a></code> performed
by calculating the precision and CV of the frequency estimates for the top
clones and by determining the proportion of the top clones whose true clonal
frequency lies in the 95-percent CI determined by <code><a rd-options='' href='freq_estimate'>freq_estimate</a></code>


freq_eval: Calculate the precision, CV, and accuracy of frequency estimates

Description

Usage

Arguments

Value