dual_eval {alphabetr}

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