Import BIOM data

Import data from BIOM 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::makeTreeSEFromBiom for documentation.

Usage

importBIOM(
  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::makeTreeSEFromBiom

Value

A MbioDataset

Examples

rich_dense_file = system.file("extdata", "rich_dense_otu_table.biom",
                               package = "biomformat")

mbioDataset <- importBIOM(
     normalizationMethod = "none", 
     keepRawValues = TRUE, 
     verbose = TRUE, 
     rich_dense_file
)

rich_dense_biom = biomformat::read_biom(rich_dense_file)

mbioDataset <- importBIOM(
     normalizationMethod = "none", 
     keepRawValues = TRUE, 
     verbose = TRUE, 
     rich_dense_biom
)