Generate a relative abundance table using kracken2/bracken data.

Usage

rel_abund_bracken(path, remove_human)

Arguments

path: The filepath to bracken data in .txt format.
remove_human: Logical. Choose to remove human samples.

Value

A tibble.

Examples

bracken <- system.file("extdata/bracken", package = "bubbler")
rel_abund_bracken(bracken)
#> # A tibble: 9,200 × 3
#>    sample_id taxon                                  rel_abund
#>    <chr>     <chr>                                      <dbl>
#>  1 20_S91    Stenotrophomonas sp. LM091           0.000206   
#>  2 20_S91    Stenotrophomonas sp. 364             0.0000245  
#>  3 20_S91    Stenotrophomonas sp. 169             0.000000670
#>  4 20_S91    Stenotrophomonas sp. Pemsol          0.000000168
#>  5 20_S91    Stenotrophomonas sp. DR822           0.000000168
#>  6 20_S91    Stenotrophomonas sp. NA06056         0.000000168
#>  7 20_S91    Stenotrophomonas sp. SXG-1           0.000000168
#>  8 20_S91    Stenotrophomonas rhizophila          0.0000106  
#>  9 20_S91    Stenotrophomonas maltophilia         0.00000452 
#> 10 20_S91    Stenotrophomonas sp. SAU14A_NAIMI4_5 0.000000335
#> # ℹ 9,190 more rows