Description Usage Arguments Details Value References See Also Examples
QIIME produces several files that can be directly imported by
the phyloseq-package
.
Originally, QIIME produced its own custom format table
that contained both OTU-abundance
and taxonomic identity information.
This function is still included in phyloseq mainly to accommodate these
now-outdated files. Recent versions of QIIME store output in the
biom-format, an emerging file format standard for microbiome data.
If your data is in the biom-format, if it ends with a .biom
file name extension, then you should use the import_biom
function instead.
1 2 3 4 | import_qiime(otufilename = NULL, mapfilename = NULL,
treefilename = NULL, refseqfilename = NULL,
refseqFunction = readDNAStringSet, refseqArgs = NULL,
parseFunction = parse_taxonomy_qiime, verbose = TRUE, ...)
|
otufilename |
(Optional). A character string indicating
the file location of the OTU file.
The combined OTU abundance and taxonomic identification file,
tab-delimited, as produced by QIIME under default output settings.
Default value is |
mapfilename |
(Optional). The QIIME map file is required
for processing barcoded primers in QIIME
as well as some of the post-clustering analysis. This is a required
input file for running QIIME. Its strict formatting specification should be
followed for correct parsing by this function.
Default value is |
treefilename |
(Optional). Default value is |
refseqfilename |
(Optional). Default |
refseqFunction |
(Optional).
Default is |
refseqArgs |
(Optional).
Default |
parseFunction |
(Optional). An optional custom function for parsing the
character string that contains the taxonomic assignment of each OTU.
The default parsing function is |
verbose |
(Optional). A |
... |
Additional arguments passed to |
Other related files include
the mapping-file that typically stores sample covariates,
converted naturally to the
sample_data-class
component data type in the phyloseq-package.
QIIME may also produce a
phylogenetic tree with a tip for each OTU, which can also be imported
specified here or imported separately using read_tree
.
See "http://www.qiime.org/" for details on using QIIME. While there are many complex dependencies, QIIME can be downloaded as a pre-installed linux virtual machine that runs “off the shelf”.
The different files useful for import to phyloseq are not collocated in a typical run of the QIIME pipeline. See the main phyloseq vignette for an example of where ot find the relevant files in the output directory.
A phyloseq-class
object.
“QIIME allows analysis of high-throughput community sequencing data.” J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Pena, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld and Rob Knight; Nature Methods, 2010; doi:10.1038/nmeth.f.303
1 2 3 4 | otufile <- system.file("extdata", "GP_otu_table_rand_short.txt.gz", package="phyloseq")
mapfile <- system.file("extdata", "master_map.txt", package="phyloseq")
trefile <- system.file("extdata", "GP_tree_rand_short.newick.gz", package="phyloseq")
import_qiime(otufile, mapfile, trefile)
|
Processing map file...
Processing otu/tax file...
Reading file into memory prior to parsing...
Detecting first header line...
Header is on line 2
Converting input file to a table...
Defining OTU table...
Parsing taxonomy table...
Processing phylogenetic tree...
/usr/local/lib/R/site-library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
phyloseq-class experiment-level object
otu_table() OTU Table: [ 500 taxa and 26 samples ]
sample_data() Sample Data: [ 26 samples by 7 sample variables ]
tax_table() Taxonomy Table: [ 500 taxa by 7 taxonomic ranks ]
phy_tree() Phylogenetic Tree: [ 500 tips and 499 internal nodes ]
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.