qza_to_tse: Generates a TreeSummarizedExperiment (TSE) object from .qza...

In jbisanz/qiime2R: qiime2R

Generates a TreeSummarizedExperiment (TSE) object from .qza artifacts TreeSummarizedExperiment

Description

Construct a TreeSummarizedExperiment object from multiple qiime2 artifacts (.qza). Embedded metadata for provenance is not maintained in this function and instead read_qza() should be used.

Usage

qza_to_tse(features, tree, taxonomy, metadata, tmp)

Arguments

features	file path for artifact containing a feature (OTU/SV) table
tree	file path for artifact containing a tree
taxonomy	file path for artifact containg taxonomy
metadata	file path for a qiime2-compliant TSV metadata file
tmp	a temporary directory that the object will be decompressed to.

Value

a TreeSummarizedExperiment object TreeSummarizedExperiment

Examples

# (Data is from tutorial
https://docs.qiime2.org/2020.2/tutorials/moving-pictures/)

tse <-qza_to_tse(
features="path_to_table.qza",
tree="path_to_rooted-tree.qza",
taxonomy="path_to_taxonomy.qza",
metadata = "path_to_sample-metadata.tsv"
)

jbisanz/qiime2R documentation built on April 24, 2024, 5 p.m.