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Aggregate odds ratios to isodecoder level.

Source: R/odds-ratios.R
aggregate_or_isodecoder.Rd

Collapse per-gene odds ratios to isodecoder level by removing gene copy numbers from the reference name and summarizing across copies.

Usage

aggregate_or_isodecoder(data, pattern = "-\\d+-\\d+$")

Arguments

data

A tibble with columns ref, pos1, pos2, log_or_clean (from clean_odds_ratios()), p_value, and total_obs.

pattern

Regular expression used to strip gene copy numbers from ref. Default "-\\d+-\\d+$" matches trailing -<copy>-<gene> suffixes.

Value

A tibble with columns: isodecoder, pos1, pos2, mean_or, mean_log_or, sd_log_or, min_pval, total_reads, and n_copies.

Examples

df <- tibble::tibble(
  ref = c("tRNA-Ala-AGC-1-1", "tRNA-Ala-AGC-2-1"),
  pos1 = c(20, 20),
  pos2 = c(34, 34),
  odds_ratio = c(2.5, 3.0),
  log_or_clean = c(0.92, 1.10),
  p_value = c(0.001, 0.01),
  total_obs = c(200, 150)
)
aggregate_or_isodecoder(df)
#> # A tibble: 1 × 9
#>   isodecoder    pos1  pos2 mean_or mean_log_or sd_log_or min_pval total_reads
#>   <chr>        <dbl> <dbl>   <dbl>       <dbl>     <dbl>    <dbl>       <dbl>
#> 1 tRNA-Ala-AGC    20    34    2.75        1.01     0.127    0.001         350
#> # ℹ 1 more variable: n_copies <int>