Import now legacy-format QIIME OTU table as a list of two matrices.
Now a legacy-format, older versions of QIIME
produced an OTU file that typically contains both OTU-abundance
and taxonomic identity information in a tab-delimted table.
If your file ends with the extension
.biom, or if you happen to know
that it is a biom-format file, or if you used default settings in a version
of QIIME of
1.7 or greater,
then YOU SHOULD USE THE BIOM-IMPORT FUNCTION instead,
(Required). The path to the qiime-formatted file you want to
import into R. Can be compressed (e.g.
(Optional). An optional custom function for parsing the
character string that contains the taxonomic assignment of each OTU.
The default parsing function is
(Optional). Logical. Should the parsing be performed in
parallel?. Default is
This function uses chunking to perform both the reading and parsing in blocks of optional size, thus constrain the peak memory usage. feature should make this importer accessible to machines with modest memory, but with the caveat that the full numeric matrix must be a manageable size at the end, too. In principle, the final tables will be large, but much more efficiently represented than the character-stored numbers. If total memory for storing the numeric matrix becomes problematic, a switch to a sparse matrix representation of the abundance – which is typically well-suited to this data – might provide a solution.
A list of two matrices.
$otutab contains the OTU Table
as a numeric matrix, while
$taxtab contains a character matrix
of the taxonomy assignments.
otufile <- system.file("extdata", "GP_otu_table_rand_short.txt.gz", package="phyloseq") import_qiime_otu_tax(otufile)