dual_tail

Matrix recording which alpha chains appear in each well of the
data. See <code><a rd-options="" href="/link/create_data?package=alphabetr&version=0.2.2" data-mini-rdoc="alphabetr::create_data">create_data</a></code>.

alpha

Matrix recording which beta chains appear in the each well of the
data. See <code><a rd-options="" href="/link/create_data?package=alphabetr&version=0.2.2" data-mini-rdoc="alphabetr::create_data">create_data</a></code>.

beta

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_results

Vector containing the number of cells sampled in the wells
of each column of the plates.

numb_cells


<code>dual_tail()</code> distinguishes between clones that share a common beta
   chain and dual TCR clones with two productive alpha chains. The procedure
   tests the null hypothesis that two candidate alpha, beta pairs with the
   same beta represent two separate clones by using the frequency estimates
   to calculate the number of wells that both clones are expected to be in.
   This is compared to the actual number of wells that both clones appear in,
   and if the actual number is greater than the expected number, than the
   pairs are chosen to represent a dual TCR clone.


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

dual_tail function

Matrix recording which alpha chains appear in each well of the
data. See <code><a rd-options='' href='create_data'>create_data</a></code>.

Matrix recording which beta chains appear in the each well of the
data. See <code><a rd-options='' href='create_data'>create_data</a></code>.

Output of <code><a rd-options='' href='freq_estimate'>freq_estimate</a></code>.

dual_tail: Discriminate between beta-sharing clones and dual-alpha TCR clones (optimized for rare clones)

Description

Usage

Arguments

Value