qiime2meco: Transform 'QIIME2' results to 'microtable' object.

In file2meco: Transform Files to 'microtable' Object with 'microeco' Package

Transform 'QIIME2' results to 'microtable' object.

Description

Transform 'QIIME2' qza results to microtable object.

Usage

qiime2meco(
  feature_table,
  sample_table = NULL,
  match_table = NULL,
  taxonomy_table = NULL,
  phylo_tree = NULL,
  rep_fasta = NULL,
  ...
)

Arguments

feature_table	the ASV abundance data with qza format, such as the 'data2_table.qza' in the example.
sample_table	default NULL; the sample metadata table; four types of formats are available: 1) q2-type tab seperated file of QIIME2, such as the 'sample-metadata.tsv' in the example; 2) comma seperated file with the suffix csv or tab seperated file with suffix tsv or txt; 3) Excel type file with the suffix xlsx or xls; require readxl package to be installed; 4) data.frame object from R.
match_table	default NULL; a two column table used to replace the sample names in feature table; Must be two columns without column names; The first column must be raw sample names same with those in feature table, the second column must be new sample names same with the rownames in sample_table; Please also see the example files. If provided, must be one of the several types of formats: 1) comma seperated file with the suffix csv or tab seperated file with suffix tsv or txt; 2) Excel type file with the suffix xlsx or xls; require readxl package to be installed; 3) data.frame object from R.
taxonomy_table	default NULL; the taxonomy assignment data with qza format, such as the 'taxonomy.qza' in the example.
phylo_tree	default NULL; the phylogenetic tree with qza format, such as the 'tree.qza' in the example.
rep_fasta	default NULL; the representative sequences with qza format, such as the 'dada2_rep_set.qza' in the example.
...	parameter passed to microtable$new function of microeco package, such as auto_tidy parameter.

Value

microtable object.

Examples

## Not run: 
# The data files is downloaded from https://docs.qiime2.org/2020.8/tutorials/pd-mice/ 
#   and stored inside the package.
abund_file_path <- system.file("extdata", "dada2_table.qza", package="file2meco")
sample_file_path <- system.file("extdata", "sample-metadata.tsv", package="file2meco")
taxonomy_file_path <- system.file("extdata", "taxonomy.qza", package="file2meco")
qiime2meco(abund_file_path)
qiime2meco(abund_file_path, sample_table = sample_file_path)
qiime2meco(abund_file_path, sample_table = sample_file_path, 
  taxonomy_table = taxonomy_file_path)

## End(Not run)

file2meco documentation built on Nov. 10, 2023, 9:09 a.m.