biomformat: observation_metadata-methods – R documentation

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observation_metadata-methods

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)

## S4 method for signature 'biom,missing'
observation_metadata(x, rows, parallel = FALSE)

## S4 method for signature 'biom,character'
observation_metadata(x, rows, parallel = FALSE)

## S4 method for signature 'biom,numeric'
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)

biomformat

An interface package for the BIOM file format

v1.18.0

GPL-2

Authors

Paul J. McMurdie <mcmurdie@stanford.edu> and Joseph N Paulson <jpaulson@jimmy.harvard.edu>

Initial release

2016-04-16