Compare Immune Repertoires

The Compare Immune Repertoires tool contrasts properties of immune repertoires, such as diversity and similarity.

To run Compare Immune Repertoires go to the Toolbox and select:

        Tools | QIAseq Panel Expert Tools (Image qiaseq_expert_folder_closed_16_n_p) | Immune Repertoire Expert Tools (Image immune_rept_folderclosed_16_n_p) | Compare Immune Repertoires (Image immune_rept_compare_16_n_p)

This opens a dialog where TCR clonotypes (Image tcr_table_16_n_p) or BCR clonotypes (Image bcr_table_16_n_p) to be compared can be selected. Note that TCR and BCR clonotypes cannot be mixed and only one type should be used at a time.

Output from Compare Immune Repertoires tool

Three outputs can be generated by the tool:

CIR Report

The report contains the following sections:

The remaining information in the report is give per chain type and only for those chain types for which clonotypes have been identified for at least two of the inputs.

Heat map

For each pair of inputs, the weighted Jaccard similarity between the two is computed. Let $ X_i$, $ Y_i$ denote the relative frequencies of the $ i$'th clonotype in the first and second input respectively. The weighted Jaccard similarity is defined as,

$\displaystyle J(X,Y) = \frac{\sum_{i=1}^n \operatorname{min}(X_i, Y_i)}{\sum_{i=1}^n \operatorname{max}(X_i, Y_i)}   .$ (8.1)

The weighted Jaccard distance is defined as,

$\displaystyle D(X,Y) = 1-J(X,Y)   .$

The heat map shows the Jaccard distance with inputs clustered hierarchically.

Similarity table

A table showing the Jaccard similarity (eq. 8.1) between each pair of inputs.