Compute charging ratio differences between conditions. — compute_charging

Compare per-tRNA charging ratios (charged / total) between two conditions, summarizing replicates with mean and standard error and computing the between-condition difference with propagated SE.

Usage

compute_charging_diffs(
  charging_data,
  condition_col = "condition",
  numerator,
  denominator,
  min_count = 50,
  n_top = NULL
)

Arguments

charging_data: A tibble from read_charging_multi() with an added condition column. Must contain ref, counts_charged, counts_uncharged, sample_id, and the column named by condition_col.
condition_col: Column name (string) for condition labels. Default "condition".
numerator: Value of condition_col for the numerator condition.
denominator: Value of condition_col for the denominator condition.
min_count: Minimum total reads (charged + uncharged) per tRNA per sample to include. Default 50.
n_top: If non-NULL, keep only the top n_top tRNAs by total abundance across all samples. Default NULL (keep all).

Value

A tibble with columns:

ref: tRNA identifier (factor ordered by diff).
ratio_numerator: Mean charging ratio for the numerator condition.
ratio_denominator: Mean charging ratio for the denominator condition.
se_numerator: Standard error of the numerator ratio.
se_denominator: Standard error of the denominator ratio.
diff: Difference: ratio_numerator - ratio_denominator.
se_diff: Propagated SE: sqrt(se_numerator^2 + se_denominator^2).

Examples

config_path <- clover_example("ecoli/config.yaml")
results <- read_pipeline_results(config_path, types = "charging")
charging <- results$charging
charging$condition <- ifelse(
  grepl("ctl", charging$sample_id), "ctl", "inf"
)
compute_charging_diffs(
  charging,
  numerator = "inf",
  denominator = "ctl"
)
#> # A tibble: 88 × 7
#>    ref     ratio_numerator ratio_denominator se_numerator se_denominator    diff
#>    <fct>             <dbl>             <dbl>        <dbl>          <dbl>   <dbl>
#>  1 host-t…           0.552             0.581       0.0503         0.0177 -0.0282
#>  2 host-t…           0.462             0.509       0.0550         0.0109 -0.0477
#>  3 host-t…           0.533             0.601       0.0572         0.0383 -0.0679
#>  4 host-t…           0.622             0.659       0.0359         0.0547 -0.0362
#>  5 host-t…           0.447             0.521       0.0546         0.0101 -0.0748
#>  6 host-t…           0.585             0.679       0.0641         0.0292 -0.0940
#>  7 host-t…           0.624             0.706       0.0530         0.0465 -0.0826
#>  8 host-t…           0.601             0.686       0.0541         0.0313 -0.0849
#>  9 host-t…           0.594             0.705       0.0510         0.0173 -0.111 
#> 10 host-t…           0.330             0.436       0.0491         0.0419 -0.106 
#> # ℹ 78 more rows
#> # ℹ 1 more variable: se_diff <dbl>