Filter Immune Repertoire

The Filter Immune Repertoire tool can be used to restrict clonotypes to only a specific subset, for example, only productive clonotypes, or clonotypes with a specific chain. Alternatively, the clonotypes can be filtered by creating a new element from a selection in the clonotypes table (Clonotypes Table).

To run Filter Immune Repertoire go to the Toolbox and select:

        Toolbox | Biomedical Genomics Analysis (Image biomedical_folder_closed_16_n_p) | Immune Repertoire Analysis (Image immune_rept_folderclosed_16_n_p) | Filter Immune Repertoire (Image filter_immune_rept_16_n_p)

This opens a dialog where a TCR clonotypes element (Image tcr_table_16_n_p) or BCR clonotypes element (Image bcr_table_16_n_p) can be selected. Click Next to navigate through the different dialogs and configure the execution (see figures 7.87.9, and 7.10).

Image filter_general
Figure 7.8: The default settings in the General filtering dialog.

Image filter_high_freq
Figure 7.9: The default settings in the High frequency filtering dialog.

Image filter_low_freq
Figure 7.10: The default settings in the Low frequency filtering dialog.

Multiple filter options can be selected to obtain the desired output. Note that the filters are applied independently.

The tool outputs the filtered clonotypes and a report summarizing statistics of the filtered clonotypes, see Output from the Immune Repertoire Analysis for details.