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

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

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)

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 = "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
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)

Example output

NULL
NULL
           taxonomy1         taxonomy2              taxonomy3
GG_OTU_1 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
GG_OTU_2 k__Bacteria  p__Cyanobacteria    c__Nostocophycideae
GG_OTU_3  k__Archaea  p__Euryarchaeota     c__Methanomicrobia
GG_OTU_4 k__Bacteria     p__Firmicutes          c__Clostridia
GG_OTU_5 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
                    taxonomy4             taxonomy5         taxonomy6
GG_OTU_1 o__Enterobacteriales f__Enterobacteriaceae    g__Escherichia
GG_OTU_2        o__Nostocales        f__Nostocaceae g__Dolichospermum
GG_OTU_3 o__Methanosarcinales f__Methanosarcinaceae g__Methanosarcina
GG_OTU_4   o__Halanaerobiales   f__Halanaerobiaceae  g__Halanaerobium
GG_OTU_5 o__Enterobacteriales f__Enterobacteriaceae    g__Escherichia
                               taxonomy7
GG_OTU_1                             s__
GG_OTU_2                             s__
GG_OTU_3                             s__
GG_OTU_4 s__Halanaerobiumsaccharolyticum
GG_OTU_5                             s__
           taxonomy1        taxonomy2           taxonomy3            taxonomy4
GG_OTU_2 k__Bacteria p__Cyanobacteria c__Nostocophycideae        o__Nostocales
GG_OTU_3  k__Archaea p__Euryarchaeota  c__Methanomicrobia o__Methanosarcinales
GG_OTU_4 k__Bacteria    p__Firmicutes       c__Clostridia   o__Halanaerobiales
                     taxonomy5         taxonomy6
GG_OTU_2        f__Nostocaceae g__Dolichospermum
GG_OTU_3 f__Methanosarcinaceae g__Methanosarcina
GG_OTU_4   f__Halanaerobiaceae  g__Halanaerobium
                               taxonomy7
GG_OTU_2                             s__
GG_OTU_3                             s__
GG_OTU_4 s__Halanaerobiumsaccharolyticum
           taxonomy1        taxonomy2           taxonomy3     taxonomy4
GG_OTU_2 k__Bacteria p__Cyanobacteria c__Nostocophycideae o__Nostocales
              taxonomy5         taxonomy6 taxonomy7
GG_OTU_2 f__Nostocaceae g__Dolichospermum       s__
           taxonomy1        taxonomy2          taxonomy3            taxonomy4
GG_OTU_3  k__Archaea p__Euryarchaeota c__Methanomicrobia o__Methanosarcinales
GG_OTU_4 k__Bacteria    p__Firmicutes      c__Clostridia   o__Halanaerobiales
                     taxonomy5         taxonomy6
GG_OTU_3 f__Methanosarcinaceae g__Methanosarcina
GG_OTU_4   f__Halanaerobiaceae  g__Halanaerobium
                               taxonomy7
GG_OTU_3                             s__
GG_OTU_4 s__Halanaerobiumsaccharolyticum
           taxonomy1         taxonomy2              taxonomy3
GG_OTU_1 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
GG_OTU_2 k__Bacteria  p__Cyanobacteria    c__Nostocophycideae
GG_OTU_3  k__Archaea  p__Euryarchaeota     c__Methanomicrobia
GG_OTU_4 k__Bacteria     p__Firmicutes          c__Clostridia
GG_OTU_5 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
                    taxonomy4             taxonomy5         taxonomy6
GG_OTU_1 o__Enterobacteriales f__Enterobacteriaceae    g__Escherichia
GG_OTU_2        o__Nostocales        f__Nostocaceae g__Dolichospermum
GG_OTU_3 o__Methanosarcinales f__Methanosarcinaceae g__Methanosarcina
GG_OTU_4   o__Halanaerobiales   f__Halanaerobiaceae  g__Halanaerobium
GG_OTU_5 o__Enterobacteriales f__Enterobacteriaceae    g__Escherichia
                               taxonomy7
GG_OTU_1                             s__
GG_OTU_2                             s__
GG_OTU_3                             s__
GG_OTU_4 s__Halanaerobiumsaccharolyticum
GG_OTU_5                             s__
           taxonomy1         taxonomy2              taxonomy3
GG_OTU_1 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
GG_OTU_2 k__Bacteria  p__Cyanobacteria    c__Nostocophycideae
GG_OTU_3  k__Archaea  p__Euryarchaeota     c__Methanomicrobia
GG_OTU_4 k__Bacteria     p__Firmicutes          c__Clostridia
GG_OTU_5 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
                    taxonomy4             taxonomy5         taxonomy6
GG_OTU_1 o__Enterobacteriales f__Enterobacteriaceae    g__Escherichia
GG_OTU_2        o__Nostocales        f__Nostocaceae g__Dolichospermum
GG_OTU_3 o__Methanosarcinales f__Methanosarcinaceae g__Methanosarcina
GG_OTU_4   o__Halanaerobiales   f__Halanaerobiaceae  g__Halanaerobium
GG_OTU_5 o__Enterobacteriales f__Enterobacteriaceae    g__Escherichia
                               taxonomy7
GG_OTU_1                             s__
GG_OTU_2                             s__
GG_OTU_3                             s__
GG_OTU_4 s__Halanaerobiumsaccharolyticum
GG_OTU_5                             s__
           taxonomy1         taxonomy2              taxonomy3
GG_OTU_1 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
GG_OTU_2 k__Bacteria  p__Cyanobacteria    c__Nostocophycideae
GG_OTU_3  k__Archaea  p__Euryarchaeota     c__Methanomicrobia
GG_OTU_4 k__Bacteria     p__Firmicutes          c__Clostridia
GG_OTU_5 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
                    taxonomy4             taxonomy5         taxonomy6
GG_OTU_1 o__Enterobacteriales f__Enterobacteriaceae    g__Escherichia
GG_OTU_2        o__Nostocales        f__Nostocaceae g__Dolichospermum
GG_OTU_3 o__Methanosarcinales f__Methanosarcinaceae g__Methanosarcina
GG_OTU_4   o__Halanaerobiales   f__Halanaerobiaceae  g__Halanaerobium
GG_OTU_5 o__Enterobacteriales f__Enterobacteriaceae    g__Escherichia
                               taxonomy7
GG_OTU_1                             s__
GG_OTU_2                             s__
GG_OTU_3                             s__
GG_OTU_4 s__Halanaerobiumsaccharolyticum
GG_OTU_5                             s__

biom documentation built on Jan. 15, 2017, 9:30 a.m.