Filter odds ratios for structure linkage arcs.

Convenience filter for odds ratio data that returns a tibble ready for the linkages parameter of plot_tRNA_structure(). Filters by p-value, observation count, and log odds ratio magnitude, then selects the columns needed for plotting.

Usage

filter_linkages(data, max_p = 0.01, min_obs = 100, min_lor = 1)

Arguments

data

A tibble of odds ratio data, typically from clean_odds_ratios(), with columns pos1, pos2, log_odds_ratio, p_value, and total_obs.

max_p

Maximum p-value to retain. Default 0.01.

min_obs

Minimum total observations to retain. Default 100.

min_lor

Minimum absolute log odds ratio to retain. Default 1.0.

Value

A tibble with columns pos1, pos2, and value (the log odds ratio), ready for plot_tRNA_structure().

Examples

df <- tibble::tibble(
  pos1 = c(20, 34, 10),
  pos2 = c(34, 58, 45),
  odds_ratio = c(4.0, 0.3, 1.1),
  log_odds_ratio = c(1.4, -1.2, 0.1),
  p_value = c(0.001, 0.005, 0.5),
  total_obs = c(200, 150, 50)
)
filter_linkages(df)
#> # A tibble: 2 × 3
#>    pos1  pos2 value
#>   <dbl> <dbl> <dbl>
#> 1    20    34   1.4
#> 2    34    58  -1.2