Check a Joint Microbiome-Metabolome Dataset

Validate cross-omics sample links and optional feature/pathway link tables.

Usage

check_crossomics_dataset(
  microbiome_data,
  metabolome_data,
  sample_link,
  feature_link = NULL,
  pathway_link = NULL
)

Arguments

microbiome_data

A microbiome_dataset object.

metabolome_data

A mass_dataset object.

sample_link

A sample link table.

feature_link

Optional feature link table.

pathway_link

Optional pathway link table.

Value

"all good." when the inputs are valid, otherwise an error string.

Examples

data("global_patterns", package = "microbiomedataset")

metabolome_expression <- as.data.frame(matrix(
  seq_len(4 * ncol(global_patterns@expression_data)),
  nrow = 4,
  ncol = ncol(global_patterns@expression_data)
))
rownames(metabolome_expression) <- paste0("M", seq_len(nrow(metabolome_expression)))
colnames(metabolome_expression) <- global_patterns@sample_info$sample_id

metabolome_data <- massdataset::create_mass_dataset(
  expression_data = metabolome_expression,
  sample_info = global_patterns@sample_info,
  variable_info = data.frame(variable_id = rownames(metabolome_expression))
)
sample_link <- data.frame(
  microbiome_sample_id = global_patterns@sample_info$sample_id,
  metabolome_sample_id = global_patterns@sample_info$sample_id
)

check_crossomics_dataset(
  microbiome_data = global_patterns,
  metabolome_data = metabolome_data,
  sample_link = sample_link
)
#> [1] "all good."