create_clones {alphabetr}

Create a synthetic set of clones with a specific underlying clonal structure

Description

create_clones() creates a set of (beta1, beta2, alpha1, alpha2) quadruples that represent the indices of the chains of clones. The function will take a fixed number of unique beta chains that are in the T cell population, and then use the degree of beta and alpha sharing to determine the number of unique alpha chains in the populations. These chains will then be randomly assigned to each other, with a proportion of them being dual TCR clones (i.e. alpha1 != alpha2 and/or beta1 != beta2), forming our random list of clones with their chain indices.

Usage

create_clones(numb_beta, dual_beta, dual_alpha, alpha_sharing, beta_sharing)

Arguments

numb_beta

The number of unique betas in the clonal population

dual_beta

The proportion of clone that are dual TCRbeta clones, i.e. has two distinct beta chains

dual_alpha

The proportion of clones that are dual TCRalpha clones, i.e. has two distinct alpha chains

alpha_sharing

A vector where the ith position represents the proportion of alpha chains that are shared by i clones; alpha chains can be shared by up to 7 clones

beta_sharing

A vector where the ith position represents the proportion of beta chains that are shared by i clones; beta chains can be shared by up to 5 clones

Value

A list of four different matrices. Each matrix is has dimensions n x 4, where n is the total number of clones and each row represents the chains of a clone. Column 1 and column 2 are the beta index/indices of the beta chain(s) used by the clone. Column 3 and 4 are the alpha index/indices of the alpha chain(s) used by the clone. If a clone has a single beta chain, then col 1 and col 2 will be equal. If a clone has a single alpha chain, then col 3 and col 4 will be equal.

Examples

 # Creating a population containing 1000 beta chains; 10% of clones with
 # dual-beta TCRs and 30% of clones with dual TCRs; 75% beta shared by one
 # clone, 20% by two clones, 5% by three clones; 80% alpha chains shared by
 # one clone, 15% by two clones, and 5% by three clones

 clones <- create_clones(numb_beta = 1000,
                         dual_alpha = .3,
                         dual_beta  = .06,
                         alpha_sharing = c(0.80, 0.15, 0.05),
                         beta_sharing  = c(0.75, 0.20, 0.05))