import_qiime2 {MicrobiotaProcess} | R Documentation |
The function was designed to import the output of qiime2 and convert them to phyloseq class.
import_qiime2( otuqza, taxaqza = NULL, mapfilename = NULL, refseqqza = NULL, treeqza = NULL, build_tree = FALSE, parallel = FALSE, ... )
otuqza |
character, the file contained otu table, the ouput of qiime2. |
taxaqza |
character, the file contained taxonomy, the ouput of qiime2, default is NULL. |
mapfilename |
character, the file contained sample information, the tsv format, default is NULL. |
refseqqza |
character, the file contained refrentent sequences, default is NULL. |
treeqza |
character, the file contained the tree file, default is NULL. |
build_tree |
logical, whether building the tree, when the rownames of feature table contains the sequence, default is FALSE. |
parallel |
logical, whether parsing the column of taxonomy multi-parallel, default is FALSE. |
..., |
additional parameters, see alos |
phyloseq-class contained the argument class.
Shuangbin Xu
otuqzafile <- system.file("extdata", "table.qza", package="MicrobiotaProcess") taxaqzafile <- system.file("extdata", "taxa.qza", package="MicrobiotaProcess") mapfile <- system.file("extdata", "metadata_qza.txt", package="MicrobiotaProcess") ps <- import_qiime2(otuqza=otuqzafile, taxaqza=taxaqzafile, mapfilename=mapfile) ps