Clean up taxon names in a MultiAssayExperiment

This functional is an optional method for fixing up taxon names in a MultiAssayExperiment to be run before filter_MAE. Specifically, it removes brackets from species names, replaces species labeled as "others" with "sp." and finally replaces underscores with spaces.

Usage

clean_MAE(dat)

Arguments

dat

A MultiAssayExperiment object specially formatted as an animalcules output.

Value

An animalcules-formatted MultiAssayExperiment object with cleaned-up taxonomy nomenclature.

Examples

in_dat <- system.file("extdata/MAE_small.RDS", package = "LegATo") |> readRDS()
clean_MAE(in_dat)
#> Registered S3 method overwritten by 'rmutil':
#>   method         from
#>   print.response httr
#> A MultiAssayExperiment object of 1 listed
#>  experiment with a user-defined name and respective class.
#>  Containing an ExperimentList class object of length 1:
#>  [1] MicrobeGenetics: SummarizedExperiment with 100 rows and 50 columns
#> Functionality:
#>  experiments() - obtain the ExperimentList instance
#>  colData() - the primary/phenotype DataFrame
#>  sampleMap() - the sample coordination DataFrame
#>  `$`, `[`, `[[` - extract colData columns, subset, or experiment
#>  *Format() - convert into a long or wide DataFrame
#>  assays() - convert ExperimentList to a SimpleList of matrices
#>  exportClass() - save data to flat files