amp_import_biom: (Defunct) Import OTU table from BIOM file

In MadsAlbertsen/ampvis2: Tools for visualising amplicon data

(Defunct) Import OTU table from BIOM file

Description

Since ampvis2 v2.7.6 amp_import_biom() has been implemented directly in amp_load instead. Don't use.

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.

Usage

amp_import_biom(...)

Arguments

...	Capture and ignore all args

Value

A data frame

Author(s)

Kasper Skytte Andersen [e-mail]

See Also

amp_load, amp_import_usearch

Examples

## Not run: 
# 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)

## End(Not run)

MadsAlbertsen/ampvis2 documentation built on Jan. 28, 2024, 7:12 a.m.