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% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/allClasses.R
\docType{class}
\name{biom-class}
\alias{biom-class}
\title{The biom format data class.}
\description{
This class inherits from the \code{\link{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
\href{http://biom-format.org/documentation/biom_format.html}{the biom-format definition}.
Importantly, this means other special properties of lists,
like operations with \code{$} and single- or double-square-braces
are also supported; as-is the \code{apply}-family function
that can operate on lists.
Note that some features of the biom-format can be essentially empty,
represented by the string \code{"null"} in the file.
These fields are returned as \code{\link{NULL}} when accessed
by an accessor function.
}
\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)
}
\seealso{
The constructor, \code{\link{biom}}
Accessor functions:
\code{\link{header}},
\code{\link{biom_shape}},
\code{\link{nrow}},
\code{\link{ncol}},
\code{\link{matrix_element_type}},
\code{\link{biom_data}},
\code{\link{observation_metadata}},
\code{\link{sample_metadata}}
}
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