dual_eval: Calculate dual depths and false dual rates for simulated...
In alphabetr: Algorithms for High-Throughput Sequencing of Antigen-Specific T Cells

Description Usage Arguments Value

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.

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

`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`

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