import_biom: Import phyloseq data from biom-format file

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

Import phyloseq data from biom-format file

Description

New versions of QIIME produce a more-comprehensive and formally-defined JSON file format, called biom file format:

Usage

import_biom(BIOMfilename, 
 treefilename=NULL, refseqfilename=NULL, refseqFunction=readDNAStringSet, refseqArgs=NULL,
 parseFunction=parse_taxonomy_default, parallel=FALSE, version=1.0, ...)

Arguments

BIOMfilename	(Required). A character string indicating the file location of the BIOM formatted file. This is a JSON formatted file, specific to biological datasets, as described in http://www.qiime.org/svn_documentation/documentation/biom_format.htmlthe biom-format home page. In principle, this file should include you OTU abundance data (OTU table), your taxonomic classification data (taxonomy table), as well as your sample data, for instance what might be in your “sample map” in QIIME. A phylogenetic tree is not yet supported by biom-format, and so is a separate argument here. If, for some reason, your biom-format file is missing one of these mentioned data types but you have it in a separate file, you can first import the data that is in the biom file using this function, import_biom, and then “merge” the remaining data after you have imported with other tools using the relatively general-purpose data merging function called merge_phyloseq.
treefilename	(Optional). Default value is NULL. A file representing a phylogenetic tree or a phylo object. Files can be NEXUS or Newick format. See read_tree for more details. Also, if using a recent release of the GreenGenes database tree, try the read_tree_greengenes function – this should solve some issues specific to importing that tree. If provided, the tree should have the same OTUs/tip-labels as the OTUs in the other files. Any taxa or samples missing in one of the files is removed from all. As an example from the QIIME pipeline, this tree would be a tree of the representative 16S rRNA sequences from each OTU cluster, with the number of leaves/tips equal to the number of taxa/species/OTUs, or the complete reference database tree that contains the OTU identifiers of every OTU in your abundance table. Note that this argument can be a tree object (phylo-class) for cases where the tree has been — or needs to be — imported separately, as in the case of the GreenGenes tree mentioned earlier (coderead_tree_greengenes).
refseqfilename	(Optional). Default NULL. The file path of the biological sequence file that contains at a minimum a sequence for each OTU in the dataset. Alternatively, you may provide an already-imported XStringSet object that satisfies this condition. In either case, the names of each OTU need to match exactly the taxa_names of the other components of your data. If this is not the case, for example if the data file is a FASTA format but contains additional information after the OTU name in each sequence header, then some additional parsing is necessary, which you can either perform separately before calling this function, or describe explicitly in a custom function provided in the (next) argument, refseqFunction. Note that the XStringSet class can represent any arbitrary sequence, including user-defined subclasses, but is most-often used to represent RNA, DNA, or amino acid sequences. The only constraint is that this special list of sequences has exactly one named element for each OTU in the dataset.
refseqFunction	(Optional). Default is readDNAStringSet, which expects to read a fasta-formatted DNA sequence file. If your reference sequences for each OTU are amino acid, RNA, or something else, then you will need to specify a different function here. This is the function used to read the file connection provided as the the previous argument, refseqfilename. This argument is ignored if refseqfilename is already a XStringSet class.
refseqArgs	(Optional). Default NULL. Additional arguments to refseqFunction. See XStringSet-io for details about additional arguments to the standard read functions in the Biostrings package.
parseFunction	(Optional). A function. It must be a function that takes as its first argument a character vector of taxonomic rank labels for a single OTU and parses and names each element (an optionally removes unwanted elements). Further details and examples of acceptable functions are provided in the documentation for parse_taxonomy_default. There are many variations on taxonomic nomenclature, and naming conventions used to store that information in various taxonomic databases and phylogenetic assignment algorithms. A popular database, http://greengenes.lbl.gov/cgi-bin/nph-index.cgigreengenes, has its own custom parsing function provided in the phyloseq package, parse_taxonomy_greengenes, and more can be contributed or posted as code snippets as needed. They can be custom-defined by a user immediately prior to the the call to import_biom, and this is a suggested first step to take when trouble-shooting taxonomy-related errors during file import.
parallel	(Optional). Logical. Wrapper option for .parallel parameter in plyr-package functions. If TRUE, apply parsing functions in parallel, using parallel backend provided by foreach and its supporting backend packages. One caveat, plyr-parallelization currently works most-cleanly with multicore-like backends (Mac OS X, Unix?), and may throw warnings for SNOW-like backends. See the example below for code invoking multicore-style backend within the doParallel package. Finally, for many datasets a parallel import should not be necessary because a serial import will be just as fast and the import is often only performed one time; after which the data should be saved as an RData file using the save function.
version	(Optional). Numeric. The expected version number of the file. As the BIOM format evolves, version-specific importers may be available by adjusting the version value. Default is 1.0. Not yet implemented. Parsing of the biom-format is done mostly by the biom package now available in CRAN.
...	Additional parameters passed on to read_tree.

Details

“The biom file format (canonically pronounced ‘biome’) is designed to be a general-use format for representing counts of observations in one or more biological samples. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium candidate project.”

http://biom-format.org/

Value

A phyloseq-class object.

References

biom-format

See Also

import

import_qiime

read_tree

read_tree_greengenes

read_biom

biom_data

sample_metadata

observation_metadata

XStringSet-io

Examples

# An included example of a rich dense biom file
rich_dense_biom  <- system.file("extdata", "rich_dense_otu_table.biom",  package="phyloseq")
import_biom(rich_dense_biom,  parseFunction=parse_taxonomy_greengenes)
# An included example of a sparse dense biom file
rich_sparse_biom <- system.file("extdata", "rich_sparse_otu_table.biom", package="phyloseq")
import_biom(rich_sparse_biom, parseFunction=parse_taxonomy_greengenes)
# # # Example code for importing large file with parallel backend
# library("doParallel")
# registerDoParallel(cores=6)
# import_biom("my/file/path/file.biom", parseFunction=parse_taxonomy_greengenes, parallel=TRUE)

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.