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 dualalpha clones. The output of

pair 
The output of 
TCR 
The clonal structure of the simulated T cell population. This is
obtained by subsetting the 
number_skewed 
The number of clones represent the top proportion of
the T cell population by frequency (this is the same 
TCR_dual 
The dual clones of the simulated T cell population. This is
obtained by subsetting the 
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 bybagpipe()

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 bybagpipe()

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