biom-class: The biom format data class.

In joey711/biomformat: An interface package for the BIOM file format

The biom format data class.

Description

This class inherits from the list-class, with validity checks specific to the definition to the biom-format. Effectively this means the list must have certain index names, some elements of which must have a specific structure or value. For further details see the biom-format definition. Importantly, this means other special properties of lists, like operations with $ and single- or double-square-braces are also supported; as-is the apply-family function that can operate on lists. Note that some features of the biom-format can be essentially empty, represented by the string "null" in the file. These fields are returned as NULL when accessed by an accessor function.

See Also

The constructor, biom

Accessor functions:

header, biom_shape, nrow, ncol, matrix_element_type, biom_data, observation_metadata, sample_metadata

Examples

biom_file = system.file("extdata", "rich_sparse_otu_table.biom", package = "biomformat")
x = read_biom(biom_file)
header(x)
biom_shape(x)
nrow(x)
ncol(x)
rownames(x)
colnames(x)
matrix_element_type(x)
biom_data(x)
observation_metadata(x)
sample_metadata(x)

joey711/biomformat documentation built on Aug. 21, 2023, 2:24 p.m.