Compute distances between microbiome samples — compute_biome

compute_biome_distance() returns a dist object between samples. Input matrices must have features in rows and samples in columns. For SummarizedExperiment input, the selected assay is extracted first.

Usage

compute_biome_distance(
  x,
  assay = "counts",
  transform = "auto",
  distance = "aitchison",
  pseudocount = 1
)

Arguments

x: A numeric matrix-like object or a SummarizedExperiment::SummarizedExperiment() object.
assay: A single string naming the assay to extract when x is a SummarizedExperiment. Defaults to "counts".
transform: A single string naming the transformation to apply before distance calculation. Use "auto" to choose "clr" for Aitchison, "relative" for Bray-Curtis, and "presence_absence" for Jaccard.
distance: A single string naming the distance. Supported values are "aitchison", "bray", and "jaccard".
pseudocount: A single positive number added before CLR transformation.

Value

A dist object between samples.

Examples

counts <- matrix(c(0, 2, 4, 1, 3, 5), nrow = 3)
colnames(counts) <- c("S1", "S2")
compute_biome_distance(counts, distance = "aitchison")
#>           S1
#> S2 0.3814209