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Grab bracken data and format to tibble.
read_bracken_file.Rd
Grab bracken data and format to tibble.
Examples
fpath <- system.file("extdata/bracken",
"7_S79_kraken2_report_bracken_output.txt", package = "bubbler")
read_bracken_file(fpath)
#> # A tibble: 221 × 8
#> sample_id name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads
#> <chr> <chr> <dbl> <chr> <dbl> <dbl>
#> 1 7_S79_krake… Ente… 1352 S 1733 0
#> 2 7_S79_krake… Ente… 1351 S 8 0
#> 3 7_S79_krake… Ente… 53346 S 3 0
#> 4 7_S79_krake… Ente… 2603296 S 3 0
#> 5 7_S79_krake… Ente… 357441 S 3 0
#> 6 7_S79_krake… Ente… 1354 S 2 0
#> 7 7_S79_krake… Ente… 33945 S 2 0
#> 8 7_S79_krake… Ente… 37734 S 2 0
#> 9 7_S79_krake… Ente… 53345 S 2 0
#> 10 7_S79_krake… Ente… 1353 S 1 0
#> # ℹ 211 more rows
#> # ℹ 2 more variables: new_est_reads <dbl>, fraction_total_reads <dbl>