Convert the qiime2 output of dada2 into phyloseq object

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

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

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

Examples

if (FALSE) {
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
}