import_qiime2: Import function to load the output of qiime2.

In MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome

Description

The function was designed to import the output of qiime2 and convert them to phyloseq class.

Usage

import_qiime2(
  otuqza,
  taxaqza = NULL,
  mapfilename = NULL,
  refseqqza = NULL,
  treeqza = NULL,
  build_tree = FALSE,
  parallel = FALSE,
  ...
)

Arguments

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 alosbuild_tree.

Value

phyloseq-class contained the argument class.

Author(s)

Shuangbin Xu

Examples

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

MicrobiotaProcess documentation built on April 18, 2021, 6 p.m.