Description Usage Arguments Details Value References See Also Examples
New versions of QIIME produce a more-comprehensive and formally-defined JSON file format, called biom file format:
1 2 3 | import_biom(BIOMfilename,
treefilename=NULL, refseqfilename=NULL, refseqFunction=readDNAStringSet, refseqArgs=NULL,
parseFunction=parse_taxonomy_default, parallel=FALSE, version=1.0, ...)
|
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,
|
treefilename |
(Optional). Default value is |
refseqfilename |
(Optional). Default |
refseqFunction |
(Optional).
Default is |
refseqArgs |
(Optional).
Default |
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 |
parallel |
(Optional). Logical. Wrapper option for 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 |
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 |
... |
Additional parameters passed on to |
“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.”
A phyloseq-class
object.
1 2 3 4 5 6 7 8 9 10 | # 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)
|
phyloseq-class experiment-level object
otu_table() OTU Table: [ 5 taxa and 6 samples ]
sample_data() Sample Data: [ 6 samples by 4 sample variables ]
tax_table() Taxonomy Table: [ 5 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table() OTU Table: [ 5 taxa and 6 samples ]
sample_data() Sample Data: [ 6 samples by 4 sample variables ]
tax_table() Taxonomy Table: [ 5 taxa by 7 taxonomic ranks ]
Warning message:
system call failed: Cannot allocate memory
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