Functional profile abundance table
The functional profile abundance table displays the names of the function, along with their clan, a combined abundance.
The table displays the following columns:
- ID: internal ID the abundance tables use for ordering the samples. IDs are unique, while Names are not necessarily, so that when merging abundance tables taxa with the same ID will be combined.
- Name: the name of the taxon, specified by the reference database or the NCBI taxonomy. If the name contains the text "(Unknown)", it indicates that this taxon corresponds to a higher-level node in the taxonomy, and that this node had a significant amount of reads associated to ancestor taxons that are present in the database but were disqualified. This indicates that there was some organism in the sample for which there is no exactly matching reference in the database, but is most likely closely related to this taxon. If the name does not contain the text "(Unknown)", it means that the sample contains this exact taxon, which is present in the database.
- Clan: a collection of related Pfam entries. The relationship may be defined by similarity of sequence, structure or profile-HMM.
- Combined Abundance: total number of reads for the function across all samples
- Min, Max, Mean, Median and Std: respectively minimum, maximum, mean, median and standard deviation of the number of reads for the fucntion across all samples
- Abundance for the sample: number of reads for each sample
In the right side panel, under the tab Data, you can switch between raw and relative abundances (relative abundances are computed as the ratio between the coverage for a function in a specific sample and the amount of coverage in the sample). You can also combine absolute counts and relative abundances by selecting the Clan level in the Aggregate feature drop-down menu.
Finally, if you have previously annotated your table with Metadata (see section 7.7), you can Aggregate sample by the groups previously defined in your metadata table. This is useful when for example analyzing replicates from the same sample origin.
Under the table, the following button allows you to Create Abundance Table from Selection, i.e., to create a table containing only the selected rows.
The data can be explored using Stack charts and Sunburst plots, similarily to OTU abundance tables (see section "Visualization of the OTU abundance table").