IntegratingTCRClusters¶

Attach TCR clusters as meta columns to Seurat object

This process is used to merge the cluster assignments from TCRClustering to the Seurat object.
The cluster assignments are prefixed with S_ or M_ to indicate whether a cluster has only one unique CDR3 sequence or multiple CDR3 sequences.
Note that a cluster with S_ prefix may still have multiple cells, as the same CDR3 sequence may be shared by multiple cells.
The cluster assignments are saved in the Seurat object at TCR_Cluster column in seurat_object@meta.data in R.

Other two columns are also added to the Seurat object: TCR_Cluster_Size and TCR_Cluster_Size1. The TCR_Cluster_Size column contains the number of cells in each cluster, while the TCR_Cluster_Size1 column contains the number of unique CDR3 sequences in each cluster.

Those columns can be then used for further downstream analysis. For example, you can find the markers for the TCR cluster (i.e. S_1 vs S_2) in each seurat cluster by

[MarkersFinder.envs]
group-by = "TCR_Cluster"
ident-1 = "S_1"
ident-2 = "S_2"
each = "seurat_clusters"

Metadata¶

The metadata of the Seurat object will be updated with the TCR cluster assignments and their sizes: