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biomformat

An interface package for the BIOM file format

This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.

Functions (18)

biom-class

The biom format data class.

biom-methods

Build and return an instance of the biom-class.

biom-package

This is an R package for interfacing with the biom format.

biom_data-methods

Access main data observation matrix data from biom-class.

biom_shape-methods

The matrix dimensions of a biom-class object.

colnames-methods

Method extensions to colnames for biom-class objects.

header-methods

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-methods

Access class of data in the matrix elements of a biom-class object

ncol-methods

Method extensions to ncol for biom-class objects.

nrow-methods

Method extensions to nrow for biom-class objects.

observation_metadata-methods

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-methods

Method extensions to rownames for biom-class objects.

sample_metadata-methods

Access meta data from biom-class.

show-methods

Method extensions to show for biom objects.

write_biom

Write a biom-format v1 file, returning a biom-class.

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

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