Import Phyloseq data — importPhyloseq • MicrobiomeDB

Import data from Phyloseq results to MbioDataset. There is some loss of granularity in this process. It results in a simpler and more performant object which is compliant with the MicrobiomeDB infrastructure. See mia::makeTreeSEFromPhyloseq for documentation.

Usage

importPhyloseq(
  normalizationMethod = c("TSS", "none"),
  keepRawValues = c(TRUE, FALSE),
  verbose = c(TRUE, FALSE),
  ...
)

Arguments

normalizationMethod: Normalization method to use on they assay data. Options are "none" and "TSS". Applying TSS normalization to absolute taxonomic abundances produces relative taxonomic abundances. Default is "TSS".
keepRawValues: Keep the raw assay values as well as the normalized values.
verbose: Print messages
...: Arguments to pass to mia::makeTreeSEFromPhyloseq

Value

A MbioDataset

Examples

data(GlobalPatterns, package="phyloseq")

mbioDataset <- importPhyloseq(
     normalizationMethod = "none", 
     keepRawValues = TRUE, 
     verbose = TRUE, 
     GlobalPatterns
)