Write a BIOM formatted file containing a strollur object's data.

Write a BIOM formatted file containing your strollur::strollur objects data.

Usage

write_biom(
  data,
  file_root = NULL,
  path = NULL,
  taxonomy = TRUE,
  sequence = TRUE
)

Arguments

data: a strollur object
file_root: a string containing the root name of the output file. Default = {dataset_name}.{bin_type}.biom
path: string containing the name of directory where the files should be written. Default = current working directory.
taxonomy: logical, when TRUE if consensus taxonomies are available include them in the biom file. Default = TRUE.
sequence: logical, when TRUE if bins have a representative sequence or all bins contain a single feature sequence include the sequences in the biom file. Default = TRUE.

Value

vector of BIOM file names. One for each bin type.

Examples


if (requireNamespace("h5lite", quietly = TRUE)) {
  miseq <- strollur::miseq_sop_example()
  strollur::write_biom(miseq, tempfile())
} else {
  message(paste(
    "To use this functionality you have to install the",
    "h5lite package."
  ))
}
#> Added 2425 sequences.
#> Assigned 2425 sequence abundances.
#> Assigned 2425 sequence taxonomies.
#> Assigned 531 otu bins.
#> Assigned 2425 asv bins.
#> Assigned 63 phylotype bins.
#> Assigned 19 samples to treatments.
#> Assigned 171 samples distances.
#> Assigned 531 otu bin taxonomies.
#> Assigned 531 otu bin representative sequences.
#> Added a metadata report.
#> Added 2 resource references.
#> Added a contigs_report report.
#> [1] "/tmp/RtmptQFCni/file1d8b66528e58.otu.biom"      
#> [2] "/tmp/RtmptQFCni/file1d8b66528e58.asv.biom"      
#> [3] "/tmp/RtmptQFCni/file1d8b66528e58.phylotype.biom"