Convenience function that reads a pipeline config, discovers output files,
and loads data for the requested result types. Each result type is returned
as a combined tibble with a sample_id column.
Usage
read_pipeline_results(
config_path,
types = c("charging", "bcerror", "odds_ratios")
)Value
A named list of tibbles, one per requested type. Each tibble
includes a sample_id column identifying the source sample.
Examples
results <- read_pipeline_results(clover_example("ecoli/config.yaml"))
results$charging
#> # A tibble: 1,140 × 6
#> sample_id ref counts_charged counts_uncharged cpm_charged cpm_uncharged
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 wt-15-ctl-01 host-… 174 124 270. 193.
#> 2 wt-15-ctl-01 host-… 1173 3220 1824. 5006.
#> 3 wt-15-ctl-01 host-… 818 807 1272. 1255.
#> 4 wt-15-ctl-01 host-… 1205 3186 1873. 4953.
#> 5 wt-15-ctl-01 host-… 351 167 546. 260.
#> 6 wt-15-ctl-01 host-… 1390 2395 2161. 3723.
#> 7 wt-15-ctl-01 host-… 615 214 956. 333.
#> 8 wt-15-ctl-01 host-… 4739 13203 7367. 20525.
#> 9 wt-15-ctl-01 host-… 1167 1162 1814. 1806.
#> 10 wt-15-ctl-01 host-… 1321 2330 2054. 3622.
#> # ℹ 1,130 more rows
results$odds_ratios
#> # A tibble: 5,432 × 17
#> sample_id ref pos1 pos2 n00 n01 n10 n11 total_obs odds_ratio
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 wt-15-ctl-01 host-t… 1 2 1345 36 34 7 1422 7.69
#> 2 wt-15-ctl-01 host-t… 2 3 1477 12 40 5 1534 15.4
#> 3 wt-15-ctl-01 host-t… 3 4 1577 14 12 7 1610 65.7
#> 4 wt-15-ctl-01 host-t… 4 6 1504 8 15 3 1530 37.6
#> 5 wt-15-ctl-01 host-t… 6 7 1298 25 0 3 1326 356.
#> 6 wt-15-ctl-01 host-t… 10 11 1511 7 11 3 1532 58.9
#> 7 wt-15-ctl-01 host-t… 11 58 1417 2 8 2 1429 177.
#> 8 wt-15-ctl-01 host-t… 15 16 685 33 290 48 1056 3.44
#> 9 wt-15-ctl-01 host-t… 18 45 1006 728 73 125 1932 2.37
#> 10 wt-15-ctl-01 host-t… 24 25 1852 25 73 8 1958 8.12
#> # ℹ 5,422 more rows
#> # ℹ 7 more variables: log_odds_ratio <dbl>, se_log_or <dbl>, ci_lower <dbl>,
#> # ci_upper <dbl>, fisher_or <dbl>, p_value <dbl>, p_adjusted <dbl>