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Create a formatted MultiAssayExperiment compatible with LegATo

Source: R/create_formatted_MAE.R
create_formatted_MAE.Rd

This function takes either a counts_dat, tax_dat, and metadata_dat input OR a TreeSummarizedExperiment input and creates a specifically-formatted MAE object that is compatible for use with LegATo and animalcules. Checks are performed on inputs to ensure that they can be integrated properly.

Usage

create_formatted_MAE(
  counts_dat = NULL,
  tax_dat = NULL,
  metadata_dat = NULL,
  tree_SE = NULL
)

Arguments

counts_dat

A matrix, data.table, or data.frame consisting of microbial raw counts data. The colnames should be sample names and the rownames should be in the same order as the tax_dat entries. Not required if tree_SE is passed in.

tax_dat

A matrix, data.table, or data.frame of hierarchical taxonomic data. Should have columns such as "family", "genus", "species" with each row uniquely delineating a different taxon. The rows should be in the same order as the rows of counts_dat. Not required if tree_SE is passed in.

metadata_dat

A metadata table with rownames equivalent to the samples that are the colnames of the counts_dat. Not required if tree_SE is passed in.

tree_SE

A TreeSummarizedExperiment object with counts, taxonomy, and metadata.

Value

A MultiAssayExperiment object.

Examples

nsample <- ntaxa <- 3
counts_dat <- data.frame(
    "X123" = runif(ntaxa, 0, 500),
    "X456" = runif(ntaxa, 0, 500),
    "X789" = runif(ntaxa, 0, 500)
)
tax_dat <- data.frame(
    "class" = c("rand1", "rand2", "rand3"),
    "species" = c("rand4", "rand5", "rand6")
) |>
    as.data.frame()
# Set rownames as lowest unique taxonomic level
rownames(tax_dat) <- tax_dat$species
rownames(counts_dat) <- tax_dat$species
metadata <- data.frame(
    Sample = c("X123", "X456", "X789"),
    Group = c("A", "B", "A"),
    Var = rnorm(nsample)
)
rownames(metadata) <- metadata$Sample
out_MAE <- create_formatted_MAE(counts_dat, tax_dat, metadata)

# TreeSummarizedExperiment
tse <- TreeSummarizedExperiment::TreeSummarizedExperiment(
    assays = list(counts = counts_dat),
    colData = metadata,            
    rowData = tax_dat             
)
out_MAE_2 <- create_formatted_MAE(tree_SE = tse)
out_MAE_2
#> 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 3 rows and 3 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