qiime1meco {file2meco}

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)