Cluster contigs by germline properties

Source: R/clustering-methods.R

Cluster contigs by germline properties

cluster_germline(
  ccdb,
  segment_keys = c("v_gene", "j_gene", "chain"),
  cluster_pk = "cluster_idx"
)

Arguments

ccdb

ContigCellDB()

segment_keys

fields in contig_tbl that identify a cluster

cluster_pk

name of cluster to be added to cluster_tbl

Examples

data(ccdb_ex)
ccdb_ex = cluster_germline(ccdb_ex)
ccdb_ex$cluster_tbl
#> # A tibble: 707 × 4
#>    cluster_idx v_gene j_gene chain
#>          <int> <chr>  <chr>  <chr>
#>  1           1 TRAV1  TRAJ15 TRA  
#>  2           2 TRAV1  TRAJ18 TRA  
#>  3           3 TRAV1  TRAJ22 TRA  
#>  4           4 TRAV1  TRAJ24 TRA  
#>  5           5 TRAV1  TRAJ26 TRA  
#>  6           6 TRAV1  TRAJ33 TRA  
#>  7           7 TRAV1  TRAJ39 TRA  
#>  8           8 TRAV1  TRAJ7  TRA  
#>  9           9 TRAV10 TRAJ15 TRA  
#> 10          10 TRAV10 TRAJ23 TRA  
#> # … with 697 more rows