Compute charging ratio differences between conditions.

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

if (FALSE) { # \dontrun{
paths <- c(
  ctl1 = "ctl1.charging.cpm.tsv.gz",
  ctl2 = "ctl2.charging.cpm.tsv.gz",
  inf1 = "inf1.charging.cpm.tsv.gz",
  inf2 = "inf2.charging.cpm.tsv.gz"
)
charging <- read_charging_multi(paths)
charging$condition <- ifelse(
  grepl("ctl", charging$sample_id), "ctl", "inf"
)
diffs <- compute_charging_diffs(
  charging,
  numerator = "inf",
  denominator = "ctl"
)
} # }