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Beta diversity

Source: R/reexports-microbiomeComputations.R
betaDiv-methods.Rd

This function returns pcoa coordinates calculated from the beta diversity dissimilarity matrix.

Usage

betaDiv(
  data,
  method = c("bray", "jaccard", "jsd"),
  k = 2,
  verbose = c(TRUE, FALSE)
)

Arguments

data

AbundanceData object

method

string defining the the beta diversity dissimilarity method. Accepted values are 'bray','jaccard', and 'jsd'

k

integer determining the number of pcoa axes to return

verbose

boolean indicating if timed logging is desired

Value

ComputeResult object

Examples

betaDivOutput <- betaDiv(
     getCollection(
  microbiomeData::DiabImmune, 
  "16S (V4) Genus (Relative taxonomic abundance analysis)"), 
     method = "bray", 
     k = 2
)
#> 
#> 2024-06-26 14:27:33.211931 Received df table with 3184 samples and 674 taxa.
#> 
#> 2024-06-26 14:27:38.440407 Computed dissimilarity matrix.
#> 
#> 2024-06-26 14:27:46.646567 Finished ordination step.
#> 
#> 2024-06-26 14:27:46.656297 Beta diversity computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method = bray , k = 2 , verbose = TRUE