qiime1meco: Transform 'QIIME' results to 'microtable' object.

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

Transform 'QIIME' results to 'microtable' object.

Description

Transform 'QIIME' results to microtable object. The QIIME results refer in particular to the files of qiime1 software.

Usage

qiime1meco(
  feature_table,
  sample_table = NULL,
  match_table = NULL,
  phylo_tree = NULL,
  rep_fasta = NULL,
  ...
)

Arguments

feature_table	the otu table generated from 'QIIME'. Taxonomic information should be in the end of the file.
sample_table	default NULL; sample metadata table; 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/txt; 2) Excel type file with the suffix xlsx or xls; require readxl package to be installed; 3) 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/txt; 2) Excel type file with the suffix xlsx or xls; require readxl package to be installed; 3) data.frame object from R.
phylo_tree	default NULL; the phylogenetic tree; generally, a file with suffix "tre".
rep_fasta	default NULL; the representative sequences; a fasta file, generally with suffix "fasta" or "fna" or "fa".
...	parameter passed to microtable$new function of microeco package, such as auto_tidy parameter.

Value

microtable object.

Examples

## Not run: 
# use the raw data files stored inside the package
otu_file_path <- system.file("extdata", "otu_table_raw.txt", package="file2meco")
sample_file_path <- system.file("extdata", "sample_info.csv", package="file2meco")
phylo_file_path <- system.file("extdata", "rep_phylo.tre", package="file2meco")
rep_fasta_path <- system.file("extdata", "rep.fna", package="file2meco")
qiime1meco(otu_file_path, sample_table = sample_file_path)
qiime1meco(otu_file_path, sample_table = sample_file_path, 
  phylo_tree = phylo_file_path)
qiime1meco(otu_file_path, sample_table = sample_file_path, 
  phylo_tree = phylo_file_path, rep_fasta = rep_fasta_path)

## End(Not run)

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