An interface package for the BIOM file format

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Documentation for package ‘biomformat’ version 1.39.17

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

Help Pages

biomformat-package	biomformat: An R interface to the BIOM file format
as.data.frame.biom	Coerce a biom object to a long-format tidy data frame
as_tibble.biom	Coerce a biom object to a tidy tibble
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.
biomformat	biomformat: An R interface to the BIOM file format
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.
biom_to_SummarizedExperiment	Convert a biom object to a SummarizedExperiment
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 v2 (HDF5) 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'.
write_hdf5_biom	Write a biom object to an HDF5 (BIOM v2) file.