biomformat (version 1.0.2)

observation_metadata: Access observation (row) meta data from biom-class.

Description

Retrieve and organize meta data from biom-class, represented as a data.frame (if possible) or a list, with proper index names.

Usage

observation_metadata(x, rows, parallel = FALSE)
"observation_metadata"(x, rows, parallel = FALSE)
"observation_metadata"(x, rows, parallel = FALSE)
"observation_metadata"(x, rows, parallel = FALSE)

Arguments

x

(Required). An instance of the biom-class.

rows

(Optional). The subset of row indices described in the returned object. For large datasets, specifying the row subset here, -- rather than first creating the complete data object -- can improve speed/efficiency. This parameter can be vector of index numbers (numeric-class) or index names (character-class).

parallel

(Optional). Logical. Whether to perform the accession parsing using a parallel-computing backend supported by the plyr-package via the foreach-package.

Value

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.

Examples

min_dense_file   = system.file("extdata", "min_dense_otu_table.biom", package = "biomformat")
min_sparse_file  = system.file("extdata", "min_sparse_otu_table.biom", package = "biomformat")
rich_dense_file  = system.file("extdata", "rich_dense_otu_table.biom", package = "biomformat")
rich_sparse_file = system.file("extdata", "rich_sparse_otu_table.biom", package = "biomformat")
min_dense_file   = system.file("extdata", "min_dense_otu_table.biom", package = "biomformat")
rich_dense_char  = system.file("extdata", "rich_dense_char.biom", package = "biomformat")
rich_sparse_char  = system.file("extdata", "rich_sparse_char.biom", package = "biomformat")
# 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
observation_metadata(x1)
observation_metadata(x2)
observation_metadata(x3)
observation_metadata(x3, 2:4)
observation_metadata(x3, 2)
observation_metadata(x3, c("GG_OTU_3", "GG_OTU_4", "whoops"))
observation_metadata(x4)
observation_metadata(x5)
observation_metadata(x6)