Refine Abundance Table parameters

To run the Refine Abundance Table tool, go to:

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Metagenomics (Image wma_folder_open_flat_16_n_p) | Abundance Analysis (Image abundance_folder_closed_16_n_p) | Refine Abundance Table (Image refine_abundance_16_n_p)

Select the abundance table to be aggregated or filtered (figure 6.1). Both single and multi-sample abundance tables are supported.

Image refineabundancetableinput
Figure 6.1: Select an abundance table as input.

Click on Next to set aggregation level.

When running from the toolbox, the tool detects the taxonomy from the input and populates the Aggregation level dropdown accordingly (figure 6.2). To perform no aggregation, choose "Do not aggregate" in the dropdown.

Image refineabundancetableaggregation
Figure 6.2: The Aggregation level dropdown is populated based on input taxonomy.

When running in a workflow, a taxonomy must be selected that matches the taxonomy of the input abundance table. If the desired taxonomy is not provided in the dropdown, it is possible to choose a Custom Taxonomy and enter the level as free text.

Three types of filters can be applied after aggregation (figure 6.3):

Image refineabundancetablefilters
Figure 6.3: Filter features based on taxonomy, prevalence and abundance.

When filtering, note that the Differential Abundance Analysis tool (see Differential Abundance Analysis), assumes that rows with similar abundance will have similar parameters, and uses this to improve parameter estimates by sharing information across rows. Therefore differential abundance results for aggressively filtered tables may not be as sensitive or precise as results for tables that contain more rows.