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, clonotypes can be filtered by creating a new element from a selection in the clonotypes table (Table for Clonotypes) or the clonotype sample comparison table (Table for Clonotype Sample Comparison).

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 single TCR clonotypes (Image tcr_table_16_n_p), BCR clonotypes (Image bcr_table_16_n_p), or Clonotype Sample Comparison (Image compared_clonotypes_16_n_p) element can be selected. The following filtering options can then be configured (see figures 7.117.12, and 7.13). Note that the filters are applied independently.

Image filter_general
Figure 7.11: General filtering options for Filter Immune Repertoire.

Image filter_high_freq
Figure 7.12: High frequency filtering options for Filter Immune Repertoire.

Image filter_low_freq
Figure 7.13: Low frequency filtering options for Filter Immune Repertoire.

The tool outputs the filtered clonotypes and a report summarizing statistics of the filtered clonotypes. See Output from the Immune Repertoire Analysis for TCR clonotypes (Image tcr_table_16_n_p) and BCR clonotypes (Image bcr_table_16_n_p), or Output from Compare Immune Repertoires tool for Clonotype Sample Comparison (Image compared_clonotypes_16_n_p).