Reads a .biom file and converts it into an OTU table compatible with ampvis2. This enables support for both the QIIME and mothur bioinformatic pipelines, as both software tools can output data in the BIOM format (for mothur see make.biom). Utilises the biomformat package, so both the JSON and HDF5 versions of the BIOM format are supported.

amp_import_biom(file)

Arguments

file

Path to the .biom file.

Value

A data frame

See also

Examples

if (FALSE) { # First import the BIOM format OTU table: biom_otutable <- amp_import_biom("path/to/file.biom") # Then use amp_load() with or without metadata as normal: d <- amp_load(biom_otutable, metadata) }