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Convert Qiime2 Data into MicrobiomeStat's Data Object

Source: R/mStat_import_qiime2_as_data_obj.R
mStat_import_qiime2_as_data_obj.Rd

This function serves as a bridge between Qiime2 and MicrobiomeStat, allowing seamless integration of Qiime2 data with the powerful MicrobiomeStat analysis toolkit. It accepts various Qiime2 microbiome study-related files and converts them into a MicrobiomeStat data object.

Usage

mStat_import_qiime2_as_data_obj(
  otu_qza,
  taxa_qza = NULL,
  sam_tab = NULL,
  refseq_qza = NULL,
  tree_qza = NULL
)

Arguments

otu_qza

A feature table with observations (OTUs, ASVs, etc.) in .qza format from Qiime2.

taxa_qza

(Optional) A taxonomy assignment table in .qza format from Qiime2.

sam_tab

(Optional) A sample metadata table.

refseq_qza

(Optional) A representative sequences table in .qza format from Qiime2.

tree_qza

(Optional) A phylogenetic tree in .qza format from Qiime2.

Value

A MicrobiomeStat data object that contains the feature table, metadata, feature annotations, phylogenetic tree, and normalization status. This object is ready to be used in MicrobiomeStat's downstream analysis functions.

Details

MicrobiomeStat is a comprehensive and user-friendly tool designed for robust microbiome data analysis. The resulting data object from this function can be directly fed into a series of MicrobiomeStat's statistical tools for further analysis.

See also

MicrobiomeStat documentation for further details on how to use the returned data object.

Examples

if (FALSE) { # \dontrun{
# This function requires the `Biostrings` and `yaml` packages.
# If you encounter issues when running the example code,
# please ensure that you have installed and loaded these packages.
# library(Biostrings)
# library(yaml)
# library(biomformat)
#data_obj <- mStat_import_qiime2_as_data_obj(otu_qza = "path_to_otu.qza",
#                                             taxa_qza = "path_to_taxa.qza",
#                                              sam_tab = "path_to_sample_metadata",
#                                             refseq_qza = "path_to_refseq.qza",
#                                              tree_qza = "path_to_tree.qza",
#                                            norm.status = "Raw")

#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")
#data.obj <- mStat_import_qiime2_as_data_obj(
#     otu_qza = otuqza_file, taxa_qza = taxaqza_file,
#     sam_tab = sample_file, tree_qza = treeqza_file,
#)
} # }