Import function to read the the output of dada2 as 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
)

Arguments

otu_qza

character, file path of the feature table from qiime2.

taxa_qza

character, file path of the taxonomic table from qiime2, default NULL.

sam_tab

character, file path of the sample metadata in tsv format, default NULL.

refseq_qza

character, file path of the representative sequences from qiime2, default NULL.

tree_qza

character, file path of the phylogenetic tree from qiime2, default NULL.

Value

phyloseq::phyloseq object.

Examples

otuqza_file <- system.file(
    "extdata", "table.qza",
    package = "microbiomeMarker"
)
taxaqza_file <- system.file(
    "extdata", "taxonomy.qza",
    package = "microbiomeMarker"
)
sample_file <- system.file(
    "extdata", "sample-metadata.tsv",
    package = "microbiomeMarker"
)
treeqza_file <- system.file(
    "extdata", "tree.qza",
    package = "microbiomeMarker"
)
ps <- import_qiime2(
    otu_qza = otuqza_file, taxa_qza = taxaqza_file,
    sam_tab = sample_file, tree_qza = treeqza_file
)
ps
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 770 taxa and 34 samples ]
#> sample_data() Sample Data:       [ 34 samples by 9 sample variables ]
#> tax_table()   Taxonomy Table:    [ 770 taxa by 7 taxonomic ranks ]
#> phy_tree()    Phylogenetic Tree: [ 770 tips and 768 internal nodes ]