ImportQiime2: Import function to load the output of qiime2.

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Import function to load the output of qiime2.

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,
  parallel = FALSE,
  ...
)

mp_import_qiime2(
  otuqza,
  taxaqza = NULL,
  mapfilename = NULL,
  refseqqza = NULL,
  treeqza = NULL,
  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 reference sequences or the XStringSet object, default is NULL.
treeqza	character, the file contained the tree file or treedata object, which is the result parsed by functions of treeio, default is NULL.
parallel	logical, whether parsing the column of taxonomy multi-parallel, default is FALSE.
...	additional parameters.

Value

MPSE-class or 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")
mpse <- mp_import_qiime2(otuqza=otuqzafile, taxaqza=taxaqzafile,
                         mapfilename=mapfile)
mpse

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.