biomformat: make_biom – R documentation

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make_biom

Create a biom-class from matrix-class or data.frame.

Description

This function creates a valid instance of the biom-class from standard base-R objects like matrix-class or data.frame. This makes it possible to export any contingency table data represented in R to the biom-format, regardless of its source. The object returned by this function is appropriate for writing to a .biom file using the write_biom function. The sparse biom-format is not (yet) supported.

Usage

make_biom(data, sample_metadata = NULL, observation_metadata = NULL,
  id = NULL, matrix_element_type = "int")

Arguments

`data`	(Required). `matrix-class` or `data.frame`. A contingency table. Observations / features / OTUs / species are rows, samples / sites / libraries are columns.
`sample_metadata`	(Optional). A `matrix-class` or `data.frame` with the number of rows equal to the number of samples in `data`. Sample covariates associated with the count data. This should look like the table returned by `sample_metadata` on a valid instance of the `biom-class`.
`observation_metadata`	(Optional). A `matrix-class` or `data.frame` with the number of rows equal to the number of features / species / OTUs / genes in `data`. This should look like the table returned by `observation_metadata` on a valid instance of the `biom-class`.
`id`	(Optional). Character string. Identifier for the project.
`matrix_element_type`	(Optional). Character string. Either 'int' or 'float'

Details

The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium candidate project. Please see the biom-format home page for more details.

Value

An object of biom-class.

References

http://biom-format.org/

Examples

# import with default parameters, specify a file
biomfile = system.file("extdata", "rich_dense_otu_table.biom", package = "biomformat")
x = read_biom(biomfile)
data = biom_data(x)
data
smd = sample_metadata(x)
smd
omd = observation_metadata(x)
omd
# Make a new biom object from component data
y = make_biom(data, smd, omd)
# Won't be identical to x because of header info.
identical(x, y)
# The data components should be, though.
identical(observation_metadata(x), observation_metadata(y))
identical(sample_metadata(x), sample_metadata(y))
identical(biom_data(x), biom_data(y))
## Quickly show that writing and reading still identical.
# Define a temporary directory to write .biom files
tempdir = tempdir()
write_biom(x, biom_file=file.path(tempdir, "x.biom"))
write_biom(y, biom_file=file.path(tempdir, "y.biom"))
x1 = read_biom(file.path(tempdir, "x.biom"))
y1 = read_biom(file.path(tempdir, "y.biom"))
identical(observation_metadata(x1), observation_metadata(y1))
identical(sample_metadata(x1), sample_metadata(y1))
identical(biom_data(x1), biom_data(y1))

biomformat

An interface package for the BIOM file format

v1.18.0

GPL-2

Authors

Paul J. McMurdie <mcmurdie@stanford.edu> and Joseph N Paulson <jpaulson@jimmy.harvard.edu>

Initial release

2016-04-16