| read_qiime_otu_table {qiimer} | R Documentation |
Parse a QIIME OTU table file in "calssic" format.
read_qiime_otu_table(filepath, commented = TRUE, metadata = TRUE)
filepath |
Path to OTU table file. |
commented |
TRUE if the header line is preceeded by an additional comment line, otherwise FALSE. This is usually the case for OTU tables generated with QIIME, so we default to TRUE. |
metadata |
TRUE if the OTU table contains a metadata column, otherwise FALSE. The metadata column usually contains taxonomic assignments, and must be located on the right-hand side of the table. |
A list with four attributes: sample_ids, otu_ids, counts, and metadata, a data structure similar to that returned by the python function 'qiime.parse.parse_otu_table'. The sample_ids, otu_ids, and metadata attributes are character vectors. The counts attribute is a matrix with one column per sample_id and one row per otu_id.