qiime2meco {file2meco} | R Documentation |
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 |
sample_table |
default NULL; the sample metadata table; four types of formats are available: |
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: |
taxonomy_table |
default NULL; the taxonomy assignment data with qza format, such as the |
phylo_tree |
default NULL; the phylogenetic tree with qza format, such as the |
rep_fasta |
default NULL; the representative sequences with qza format, such as the |
... |
parameter passed to |
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)