Clean odds ratio data.

Prepare odds ratio data for downstream analysis by capping infinite log odds ratio values and optionally removing adapter positions.

Usage

clean_odds_ratios(data, cap_inf = 2)

Arguments

data

A tibble of odds ratio data with columns ref, odds_ratio, and log_odds_ratio.

cap_inf

Numeric value added to (or subtracted from) the finite range when capping positive (or negative) infinite log odds ratios. Default 2.

Value

A tibble with a new log_or_clean column where infinite values have been capped.

Examples

df <- tibble::tibble(
  ref = "tRNA-Ala-AGC-1-1",
  pos1 = c(20, 34),
  pos2 = c(34, 58),
  odds_ratio = c(2.5, Inf),
  log_odds_ratio = c(0.92, Inf),
  p_value = c(0.001, 0.01),
  total_obs = c(200, 150)
)
clean_odds_ratios(df)
#> # A tibble: 2 × 8
#>   ref        pos1  pos2 odds_ratio log_odds_ratio p_value total_obs log_or_clean
#>   <chr>     <dbl> <dbl>      <dbl>          <dbl>   <dbl>     <dbl>        <dbl>
#> 1 tRNA-Ala…    20    34        2.5           0.92   0.001       200         0.92
#> 2 tRNA-Ala…    34    58      Inf           Inf      0.01        150         2.92