import_qiime: Import function to read the now legacy-format QIIME OTU...
In phyloseq: Handling and analysis of high-throughput microbiome census data

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 This function is still included in phyloseq mainly to accommodate these now-outdated files.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.

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 `NULL`.
`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 `NULL`.
`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). An optional custom function for parsing the character string that contains the taxonomic assignment of each OTU. The default parsing function is `parse_taxonomy_qiime`, specialized for splitting the `";"`-delimited strings and also attempting to interpret greengenes prefixes, if any, as that is a common format of the taxonomy string produced by QIIME.
`verbose`	(Optional). A `logical`. Default is `TRUE`. Should progresss messages be `cat`ted to standard out?
`...`	Additional arguments passed to `read_tree`

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.

http://qiime.org/

“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

phyloseq

merge_phyloseq

read_tree

read_tree_greengenes

XStringSet-io

 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 ]