Read a per-position-pair odds ratio file produced by the tRNA sequencing pipeline. These files contain pairwise modification co-occurrence statistics.
Value
A tibble with columns including ref, pos1, pos2,
odds_ratio, log_odds_ratio, p_value, and total_obs.
Examples
path <- clover_example(
"ecoli/summary/tables/wt-15-ctl-01/wt-15-ctl-01.odds_ratios_filtered.tsv.gz"
)
read_odds_ratios(path)
#> # A tibble: 720 × 16
#> ref pos1 pos2 n00 n01 n10 n11 total_obs odds_ratio log_odds_ratio
#> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 host… 1 2 1345 36 34 7 1422 7.69 2.04
#> 2 host… 2 3 1477 12 40 5 1534 15.4 2.73
#> 3 host… 3 4 1577 14 12 7 1610 65.7 4.19
#> 4 host… 4 6 1504 8 15 3 1530 37.6 3.63
#> 5 host… 6 7 1298 25 0 3 1326 356. 5.88
#> 6 host… 10 11 1511 7 11 3 1532 58.9 4.08
#> 7 host… 11 58 1417 2 8 2 1429 177. 5.18
#> 8 host… 15 16 685 33 290 48 1056 3.44 1.23
#> 9 host… 18 45 1006 728 73 125 1932 2.37 0.861
#> 10 host… 24 25 1852 25 73 8 1958 8.12 2.09
#> # ℹ 710 more rows
#> # ℹ 6 more variables: se_log_or <dbl>, ci_lower <dbl>, ci_upper <dbl>,
#> # fisher_or <dbl>, p_value <dbl>, p_adjusted <dbl>