dual_eval {alphabetr} R Documentation

## Calculate dual depths and false dual rates for simulated alphabetr experiments

### Description

`dual_eval()` is used in simulation situations to compare the duals determined by `dual_top` and `dual_tail` (which can be combined with `rbind()`) to the duals in the simulated T cell population.

### Usage

```dual_eval(duals, pair, TCR, number_skewed, TCR_dual)
```

### Arguments

 `duals` A 4 column matrix (col 1 + 2 = beta indices, col 3 + 4 = alpha indices) containing the indices of dual-alpha clones. The output of `dual_top` and `dual_tail` are in this form (and the outputs of these two functions can combined by using `rbind()`) `pair` The output of `bagpipe` `TCR` The clonal structure of the simulated T cell population. This is obtained by subsetting the `TCR` element of the output of `create_clones` `number_skewed` The number of clones represent the top proportion of the T cell population by frequency (this is the same `number_skewed` argument used when `create_clones` is called) `TCR_dual` The dual clones of the simulated T cell population. This is obtained by subsetting the `dual_alph` element of the output of `create_clones`

### Value

A data.frame with the following columns:

• `fdr`, the false dual rate

• `numb_cand_duals`, the number of duals identified

• `adj_depth_top`, the adjusted dual depth of top clones

• `abs_depth_top`, the absolute dual depth of top clones

• `numb_correct_top`, the number of correctly identified dual clones in the top

• `numb_duals_ans_top`, the number of top dual clones in the simulated T cell population

• `numb_poss_top`, the number of top dual clones whose beta and both alpha chains were identified by `bagpipe()`

• `numb_unestimated_top`, number of top dual clones whose frequencies could not be calculated (usually because the clones appeared in every well of the data)

• `adj_depth_tail`, the adjusted dual depth of tail clones

• `abs_depth_tail`, the absolute dual depth of tail clones

• `numb_correct_tail`, the number of correctly identified tail clones

• `numb_duals_ans_tail`, the number of dual tail clones in the simulated T cell population

• `numb_poss_tail`, the number of tail dual cloens whose beta and both alpha chains were identified by `bagpipe()`

• `numb_unestimated_tail`, the number of tail clones whose frequencies could not be calculated

[Package alphabetr version 0.2.2 Index]