Compute ratio of odds ratios between conditions.

Compare modification co-occurrence between two conditions by computing the ratio of odds ratios (ROR). Replicates within each condition are aggregated using the specified function.

Usage

compute_ror(
  odds_data,
  condition_col = "condition",
  numerator,
  denominator,
  min_obs = 100,
  agg_fun = mean
)

Arguments

odds_data

A combined tibble of odds ratio data with a condition column (or column specified by condition_col) and sample_id.

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_obs

Minimum total_obs for a pair to be included. Default 100.

agg_fun

Function to aggregate replicate log odds ratios. Default mean.

Value

A tibble with columns: pos1, pos2, or_numerator, or_denominator, ror, and log_ror.

Examples

if (FALSE) { # \dontrun{
combined_or <- read_odds_ratios_multi(paths)
combined_or$condition <- ifelse(
  grepl("wt", combined_or$sample_id), "wt", "mut"
)
ror <- compute_ror(combined_or, numerator = "mut", denominator = "wt")
} # }