import_qiime2: Convert the qiime2 output of dada2 into phyloseq object

In HuaZou/MicrobiomeAnalysis: Data analysis toolkits in metagenomics

Convert the qiime2 output of dada2 into phyloseq object

Description

Import the qiime2 artifacts, including feature table, taxonomic table, phylogenetic tree, representative sequence and sample metadata into phyloseq object.

Usage

import_qiime2(
  otu_qza,
  taxa_qza = NULL,
  sam_tab = NULL,
  refseq_qza = NULL,
  tree_qza = NULL,
  keep_taxa_rows = TRUE
)

Arguments

otu_qza	(Required). character, file path of the feature table from qiime2.
taxa_qza	(Optional). character, file path of the taxonomic table from qiime2, default NULL.
sam_tab	(Optional). character, file path of the sample metadata in tsv format, default NULL.
refseq_qza	(Optional). character, file path of the representative sequences from qiime2, default NULL.
tree_qza	(Optional). character, file path of the phylogenetic tree from qiime2, default NULL.
keep_taxa_rows	(Optional). logical. whether keep taxa in rows or not in the otu_table of the returned phyloseq object, default TRUE.

Value

phyloseq::phyloseq object.

Author(s)

Created by Yang Cao; modified by Hua Zou (5/14/2022 Shenzhen China)

Examples

## Not run: 
otuqza_file <- system.file(
    "extdata", "table.qza",
    package = "MicrobiomeAnalysis"
)
taxaqza_file <- system.file(
    "extdata", "taxonomy.qza",
    package = "MicrobiomeAnalysis"
)
sample_file <- system.file(
    "extdata", "sample-metadata.tsv",
    package = "MicrobiomeAnalysis"
)
treeqza_file <- system.file(
    "extdata", "tree.qza",
    package = "MicrobiomeAnalysis"
)
ps <- import_qiime2(
    otu_qza = otuqza_file, taxa_qza = taxaqza_file,
    sam_tab = sample_file, tree_qza = treeqza_file
)
ps

## End(Not run)

HuaZou/MicrobiomeAnalysis documentation built on Dec. 12, 2023, 10:37 a.m.