Obtain a data.frame of ordered taxa abundances at a given level

This function takes a MultiAssayExperiment object and returns a data.frame of the present taxa at a user-supplied taxonomy level, and outputs the average abundances of the taxa.

Usage

get_top_taxa(dat, taxon_level = "genus")

Arguments

dat

A MultiAssayExperiment object specially formatted as an animalcules output.

taxon_level

Character string indicating the level of taxonomy to aggregate the counts data. Must be the name of a column in MultiAssayExperiment::rowData(dat).

Value

A data.frame

Examples

in_dat <- system.file("extdata/MAE_small.RDS", package = "LegATo") |> readRDS()
out <- get_top_taxa(in_dat, "genus")
out
#>                 taxon     allmeans
#> 1       Acinetobacter 4.393573e-01
#> 2     Corynebacterium 1.787561e-01
#> 3      Staphylococcus 9.218562e-02
#> 4  Noviherbaspirillum 6.755399e-02
#> 5             Kocuria 6.213396e-02
#> 6         Pseudomonas 2.661071e-02
#> 7            Brucella 2.273844e-02
#> 8    Alkalihalophilus 2.191473e-02
#> 9           Weissella 1.575164e-02
#> 10           Listeria 1.569116e-02
#> 11          Moraxella 1.527953e-02
#> 12      Streptococcus 1.295274e-02
#> 13       Enterobacter 8.513321e-03
#> 14              Other 8.108827e-03
#> 15        Haemophilus 5.898783e-03
#> 16          Aeromonas 3.512574e-03
#> 17         Paracoccus 1.746868e-03
#> 18     Dolosigranulum 5.219494e-04
#> 19         Mycoplasma 3.750489e-04
#> 20            Delftia 2.991494e-04
#> 21      Cutibacterium 7.156670e-05
#> 22        Escherichia 2.596714e-05