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.
|Author||Paul J. McMurdie <email@example.com> and the biom-format team http://biom-format.org/|
|Date of publication||2014-02-24 01:20:23|
|Maintainer||Paul J. McMurdie <firstname.lastname@example.org>|
biom-class: The biom format data class.
biom_data-methods: Access main data observation matrix data from 'biom-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_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.
matrix_element_type-methods: Access class of data in the matrix elements of a 'biom-class'...
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'.
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 file, returning a 'biom-class'.