An interface package (beta) for the BIOM file format.


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Documentation for package ‘biom’ version 0.3.12

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biom-package This is an R package for interfacing with the biom format.
biom Build and return an instance of the biom-class.
biom-class The biom format data class.
biom-method Build and return an instance of the biom-class.
biom_data Access main data observation matrix data from 'biom-class'.
biom_data-method Access main data observation matrix data from 'biom-class'.
biom_shape The matrix dimensions of a 'biom-class' object.
biom_shape-method The matrix dimensions of a 'biom-class' object.
colnames Method extensions to 'colnames' for 'biom-class' objects.
colnames-method Method extensions to 'colnames' for 'biom-class' objects.
header Extract the header from a 'biom-class' object as a list.
header-method Extract the header from a 'biom-class' object as a list.
matrix_element_type Access class of data in the matrix elements of a 'biom-class' object
matrix_element_type-method Access class of data in the matrix elements of a 'biom-class' object
ncol Method extensions to 'ncol' for 'biom-class' objects.
ncol-method Method extensions to 'ncol' for 'biom-class' objects.
nrow Method extensions to 'nrow' for 'biom-class' objects.
nrow-method Method extensions to 'nrow' for 'biom-class' objects.
observation_metadata Access observation (row) meta data from 'biom-class'.
observation_metadata-method Access observation (row) meta data from 'biom-class'.
read_biom Read a biom-format file, returning a 'biom-class'.
rownames Method extensions to 'rownames' for 'biom-class' objects.
rownames-method Method extensions to 'rownames' for 'biom-class' objects.
sample_metadata Access meta data from 'biom-class'.
sample_metadata-method Access meta data from 'biom-class'.
show Method extensions to show for biom objects.
show-method Method extensions to show for biom objects.
write_biom Write a biom-format file, returning a 'biom-class'.