Integrate Matched Microbiome and Metabolome Data — integrate_microbe

Wrapper for multiblock integration methods on matched omics matrices.

Usage

integrate_microbe_metabolite(
  object = NULL,
  microbiome_data = NULL,
  metabolome_data = NULL,
  sample_link = NULL,
  method = c("spls", "diablo"),
  microbiome_rank = "Genus",
  ncomp = 2
)

Arguments

object: A microbiome_metabolome_dataset object.
microbiome_data: A microbiome_dataset object. Used when object is not supplied.
metabolome_data: A mass_dataset object. Used when object is not supplied.
sample_link: Optional sample link table used when object is not supplied.
method: Integration method.
microbiome_rank: Taxonomy rank for microbiome aggregation.
ncomp: Number of latent components.

Value

A crossomics_integration object.

Examples

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

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

if (requireNamespace("mixOmics", quietly = TRUE)) {
  x <- integrate_microbe_metabolite(
    microbiome_data = demo_crossomics$microbiome_data,
    metabolome_data = demo_crossomics$metabolome_data,
    sample_link = demo_crossomics$sample_link,
    method = "spls"
  )
  class(x)
}
#> Warning: NaNs produced
#> [1] "crossomics_integration"
#> attr(,"package")
#> [1] "microbiomedataset"