metfile_init | R Documentation |
Initiate a metadata file that is compatible with OCMSlooksy from OCMS 16S database file or from a tab-delimited file of a count table.
metfile_init( db_file, out_dir = NULL, ref_table = NULL, id_orient = "col", dummy = NULL )
db_file |
rsqlite database file. Set to |
out_dir |
output directory. default |
ref_table |
name of table in database from which sampleID are generated.
default |
id_orient |
indicates orientation of sample IDs. default 'col' indicates samples are in columns. 'row' indicates samples are in rows and sample IDs are in the first column |
dummy |
default NULL. when string supplied, adds a dummy column of NAs with the string as the column name. |
When initiating the metadata file from a count table, set db_file
to FALSE
and count table is supplied in ref_table
as tab-delimited file. If samples are in columns, set id_orient
to 'col'.
If samples are in rows, the sample IDs should be in the first column.
function returns a dataframe . if out_dir
is set, writes the initiated metadata to file as a tab-delimited file named "metadata.tsv"
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