read_hdf5_biom: Read in a biom-format vs 2 file, returning a 'list'.

In joey711/biomformat: An interface package for the BIOM file format

Read in a biom-format vs 2 file, returning a list.

Description

This function is meant only to be used if the user knows the file is a particular version / hdf5 format. Otherwise, the 'read_biom' file should be used.

Usage

read_hdf5_biom(biom_file)

Arguments

biom_file

(Required). A biom object that is going to be written to file as a proper biom formatted file, adhering to the biom-format definition.

Value

Nothing. The first argument, x, is written to a file.

References

http://biom-format.org/

See Also

Function to create a biom object from R data, make_biom.

Definition of the biom-class.

The read_hdf5_biom import function.

Accessor functions like header.

Examples

biom_file <- system.file("extdata", "rich_sparse_otu_table_hdf5.biom", package = "biomformat")
x = read_hdf5_biom(biom_file)
x = biom(x)
outfile = tempfile()
write_biom(x, outfile)
y = read_biom(outfile)
identical(observation_metadata(x),observation_metadata(y))
identical(sample_metadata(x),sample_metadata(y))
identical(biom_data(x), biom_data(y))

joey711/biomformat documentation built on Aug. 21, 2023, 2:24 p.m.