create_clones {alphabetr} | R Documentation |

## 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))
```

*alphabetr*version 0.2.2 Index]