Create a Joint Microbiome-Metabolome Dataset — create_microbiome_metabolome

Build a paired cross-omics object from microbiome_dataset and mass_dataset, keeping an explicit sample link table between omics.

Usage

create_microbiome_metabolome_dataset(
  microbiome_data,
  metabolome_data,
  sample_link = NULL,
  feature_link = NULL,
  pathway_link = NULL,
  align_samples = TRUE
)

Arguments

microbiome_data: A microbiome_dataset object.
metabolome_data: A mass_dataset object.
sample_link: Optional data.frame with columns microbiome_sample_id and metabolome_sample_id. If missing, shared sample ids are inferred.
feature_link: Optional taxon-metabolite link table.
pathway_link: Optional pathway/reaction link table.
align_samples: Whether to prune both omics to the linked samples.

Value

A microbiome_metabolome_dataset object.

Examples

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

metabolome_expression <- as.data.frame(matrix(
  seq_len(6 * ncol(global_patterns@expression_data)),
  nrow = 6,
  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))
)

x <- create_microbiome_metabolome_dataset(
  microbiome_data = global_patterns,
  metabolome_data = metabolome_data
)
x
#> microbiome_metabolome_dataset
#> Samples linked: 26
#> Microbiome dimensions: 19216 x 26
#> Metabolome dimensions: 6 x 26