Description Usage Arguments Value Examples
Retrieve and organize meta data from
biom-class
, represented as a
data.frame
(if possible, or a list) with
proper index names.
1 | sample_metadata(x, columns, parallel=FALSE)
|
x |
(Required). An instance of the
|
columns |
(Optional). The subset of column indices
described in the returned object. For large datasets,
specifying the column subset here, rather than after
creating the whole matrix first, can improve
speed/efficiency. Can be vector of index numbers
( |
parallel |
(Optional). Logical. Whether to perform
the accession parsing using a parallel-computing backend
supported by the |
A data.frame
or list
containing the meta data, with index names. The precise
form of the object returned depends on the metadata
stored in x
. A data.frame
is created if
possible.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | min_dense_file = system.file("extdata", "min_dense_otu_table.biom", package = "biom")
min_sparse_file = system.file("extdata", "min_sparse_otu_table.biom", package = "biom")
rich_dense_file = system.file("extdata", "rich_dense_otu_table.biom", package = "biom")
rich_sparse_file = system.file("extdata", "rich_sparse_otu_table.biom", package = "biom")
min_dense_file = system.file("extdata", "min_dense_otu_table.biom", package = "biom")
rich_dense_char = system.file("extdata", "rich_dense_char.biom", package = "biom")
rich_sparse_char = system.file("extdata", "rich_sparse_char.biom", package = "biom")
# Read the biom-format files
x1 = read_biom(min_dense_file)
x2 = read_biom(min_sparse_file)
x3 = read_biom(rich_dense_file)
x4 = read_biom(rich_sparse_file)
x5 = read_biom(rich_dense_char)
x6 = read_biom(rich_sparse_char)
# Extract metadata
sample_metadata(x1)
sample_metadata(x2)
sample_metadata(x3)
sample_metadata(x3, 1:4)
sample_metadata(x4)
sample_metadata(x5)
sample_metadata(x6)
|
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