import_qiime2 {microbiomeMarker} | R Documentation |
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 )
otu_qza |
character, file path of the feature table from qiime2. |
taxa_qza |
character, file path of the taxonomic table from qiime2,
default |
sam_tab |
character, file path of the sample metadata in tsv format,
default |
refseq_qza |
character, file path of the representative sequences from
qiime2, default |
tree_qza |
character, file path of the phylogenetic tree from
qiime2, default |
phyloseq::phyloseq
object.
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