# An interface package for the BIOM file format

## Documentation for package ‘biomformat’ version 1.34.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

biom-package | This is an R package for interfacing with the biom format.
biom | Build and return an instance of the biom-class.
biom-class | The biom format data class.
biom-method | Build and return an instance of the biom-class.
biom_data | Access main data observation matrix data from 'biom-class'.
biom_data-method | Access main data observation matrix data from 'biom-class'.
biom_shape | The matrix dimensions of a 'biom-class' object.
biom_shape-method | The matrix dimensions of a 'biom-class' object.
colnames-method | Method extensions to 'colnames' for 'biom-class' objects.
header | Extract the header from a 'biom-class' object as a list.
header-method | Extract the header from a 'biom-class' object as a list.
make_biom | Create a 'biom-class' from 'matrix-class' or 'data.frame'.
matrix_element_type | Access class of data in the matrix elements of a 'biom-class' object
matrix_element_type-method | Access class of data in the matrix elements of a 'biom-class' object
ncol-method | Method extensions to 'ncol' for 'biom-class' objects.
nrow-method | Method extensions to 'nrow' for 'biom-class' objects.
observation_metadata | Access observation (row) meta data from 'biom-class'.
observation_metadata-method | Access observation (row) meta data from 'biom-class'.
read_biom | Read a biom-format file, returning a 'biom-class'.
read_hdf5_biom | Read in a biom-format vs 2 file, returning a 'list'.
rownames-method | Method extensions to 'rownames' for 'biom-class' objects.
sample_metadata | Access meta data from 'biom-class'.
sample_metadata-method | Access meta data from 'biom-class'.
show-method | Method extensions to show for biom objects.
write_biom | Write a biom-format v1 file, returning a 'biom-class'.