dual_top {alphabetr} | R Documentation |

## 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 |

`beta` |
Matrix recording which beta chains appear in the each well of the
data. See |

`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).

*alphabetr*version 0.2.2 Index]