dual_tail: Discriminate between beta-sharing clones and dual-alpha TCR...

In alphabetr: Algorithms for High-Throughput Sequencing of Antigen-Specific T Cells

Description

dual_tail() 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.

Usage

dual_tail(alpha, beta, freq_results, numb_cells)

Arguments

alpha	Matrix recording which alpha chains appear in each well of the data. See create_data.
beta	Matrix recording which beta chains appear in the each well of the data. See create_data.
freq_results	Output of freq_estimate.
numb_cells	Vector containing the number of cells sampled in the wells of each column of the plates.

Value

A n x 3 matrix where n is the number of candidate clones, column 1 is the beta index of the clone, and column 2-3 are the alpha indices of the clone

alphabetr documentation built on May 2, 2019, 12:36 p.m.