ImportQiime2 {MicrobiotaProcess} | R Documentation

## 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 by parsing function 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

[Package MicrobiotaProcess version 1.4.4 Index]