dual_top: Discriminate between beta-sharing clones and dual-alpha TCR clones (optimized for common clones)

Description

dual_top() distinguishes between clones that share a common beta chain and dual TCR clones with two productive alpha chains. The procedure calculates the likelihood that two (alpha, beta) pairs (with common a beta chain) come from two distinct clones sharing the same beta chain vs the likelihood that the two pairs derive from a dual TCR-alpha clone. A significant difference between the two likelihoods is indicative of a dual alpha clone, and these clones are returned as dual clones.

Usage

dual_top(alpha, beta, pair, error, 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.

pair

A matrix where each row is a beta/alpha pair, column 1 and 2 are the beta indices, and column 3 and 4 are the alpha indices, and column 5 is the proportion of replicates the clone was found in (or equal to -1 if the clone is dual)

error

The mean error "dropped" chain rate due to PCR or sequencing errors.

numb_cells

The number of cells per well in each column of the plates. Should be a vector of 12 elements.

Value

A matrix of dual-alpha clones, where col 1 and 2 are beta indices of the clone (which should be equal) and col 3 and 4 are alpha indices of the clone (which are different).