Runnable toy example (no DIA-NN files required)
We start with a small simulated dataset that exercises the diagFDR
functions. Any workflow producing outputs that can be mapped to the
columns id, is_decoy, q,
pep, run, and score can be
handled similarly.
library(diagFDR)
set.seed(1)
n <- 3000
toy_global <- data.frame(
id = paste0("P", seq_len(n)),
is_decoy = sample(c(FALSE, TRUE), n, replace = TRUE, prob = c(0.97, 0.03)),
q = pmin(1, runif(n)^3), # skew toward small q-values
pep = NA_real_,
run = NA_character_,
score = NA_real_
)
x_global <- as_dfdr_tbl(
toy_global,
unit = "precursor",
scope = "global",
q_source = "toy",
q_max_export = 0.5
)
diag <- dfdr_run_all(
xs = list(global = x_global),
alpha_main = 0.01,
alphas = c(1e-3, 2e-3, 5e-3, 1e-2, 2e-2, 5e-2, 1e-1, 2e-1),
low_conf = c(0.2, 0.5)
)
#> Warning: List 'global': pseudo-p-values not computed (no score column). Pass
#> `score_col` to the import function if the export has a discriminant score
#> (DIA-NN 2.x reports have no CScore column), or use `pseudo_pvalue_score =
#> "pep"` in dfdr_run_all() to use -PEP as a surrogate score.Headline stability at 1%
diag$tables$headline
#> # A tibble: 1 × 27
#> alpha T_alpha D_alpha FDR_hat support_index CV_benchmark FDR_minus1 FDR_plus1
#> <dbl> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 0.01 602 13 0.0216 0.277 0.392 0.0199 0.0233
#> # ℹ 19 more variables: FDR_minusK <dbl>, FDR_plusK <dbl>, k2sqrtD <int>,
#> # FDR_minus2sqrtD <dbl>, FDR_plus2sqrtD <dbl>, list <chr>, D_alpha_win <int>,
#> # eq_evaluable <lgl>, eq_reason <chr>, effect_abs <dbl>, IPE <dbl>,
#> # flag_Dalpha <chr>, flag_support <chr>, flag_Dwin <chr>, flag_IPE <chr>,
#> # flag_FDR <chr>, flag_equalchance <chr>, status <chr>, interpretation <chr>
Equal-chance plausibility by q-band
diag$tables$equal_chance_pooled
#> # A tibble: 1 × 12
#> qmax_export low_lo low_hi N_test N_D_test pi_D_hat effect_abs ci95_lo ci95_hi
#> <dbl> <dbl> <dbl> <int> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 0.5 0.2 0.5 596 26 0.0436 0.456 0.0299 0.0632
#> # ℹ 3 more variables: p_value_binom <dbl>, pass_minN <lgl>, list <chr>
diag$plots$equal_chance__global
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the diagFDR package.
#> Please report the issue to the authors.
#> This warning is displayed once per session.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.