import_qiime2: Import function to read the the output of dada2 as phyloseq...

In yiluheihei/microbiomeMarker: microbiome biomarker analysis toolkit

Import function to read the the output of dada2 as 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
)

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

yiluheihei/microbiomeMarker documentation built on Nov. 5, 2023, 7:19 a.m.