Questions about confidence scores

[Kevis9]

Hi, thanks for the insightful work! Now I am using scmap to annotate query data based on reference data. I wonder how to get the confidence score of the predicted cell type.

Following is my core code:

# scmap Cluster
    ref_sce <- scmap::indexCluster(ref_sce)


    scmapCluster_results <- scmapCluster(projection = query_sce,
                                         index_list = list(yan = metadata(ref_sce)$scmap_cluster_index),
                                         threshold=0)
    pred <- scmapCluster_results$scmap_cluster_labs