canonicalize_cluster {CellaRepertorium} | R Documentation

## Find a canonical contig to represent a cluster

### Description

Find a canonical contig to represent a cluster

### Usage

    canonicalize_cluster(
      ccdb,
      contig_filter_args,
      tie_break_keys = character(),
      order = 1,
      representative = ccdb$cluster_pk[1],
      contig_fields = c("cdr3", "cdr3_nt", "chain", "v_gene", "d_gene", "j_gene"),
      overwrite = TRUE
    )

### Arguments

`ccdb` | `ContigCellDB()`
`contig_filter_args` | an expression passed to `dplyr::filter()`. Unlike `filter`, multiple criteria must be `&` together, rather than using commas to separate. These act on `ccdb$contig_tbl`
`tie_break_keys` | (optional) `character` naming fields in `contig_tbl` that are used sort the contig table in descending order. Used to break ties if `contig_filter_args` does not return a unique contig for each cluster
`order` | The rank order of the contig, based on `tie_break_keys` to return. If `tie_break_keys` included an ordered factor (such as chain) this could be used to return the second chain.
`representative` | an optional field from `contig_tbl` that will be made unique. Serve as a surrogate `cluster_pk`.
`contig_fields` | Optional fields from `contig_tbl` that will be copied into the `cluster_tbl` from the canonical contig.
`overwrite` | `logical` – should non-key fields in y be overwritten using x, or should a suffix (".y") be added

### Value

`ContigCellDB()` with some number of clusters/contigs/cells but with "canonical" values copied into `cluster_tbl`

### See Also

`canonicalize_cell()` `left_join_warn()`

### Examples

    library(dplyr)
    data(ccdb_ex)
    ccdb_ex_small = ccdb_ex
    ccdb_ex_small$cell_tbl = ccdb_ex_small$cell_tbl[1:200,]
    ccdb_ex_small = cdhit_ccdb(ccdb_ex_small,
    sequence_key = 'cdr3_nt', type = 'DNA', cluster_name = 'DNA97',
    identity = .965, min_length = 12, G = 1)
    ccdb_ex_small = fine_clustering(ccdb_ex_small, sequence_key = 'cdr3_nt', type = 'DNA')

    # Canonicalize with the medoid contig is probably what is most common
    ccdb_medoid = canonicalize_cluster(ccdb_ex_small)

    # But there are other possibilities.
    # To pass multiple "AND" filter arguments must use &
    ccdb_umi = canonicalize_cluster(ccdb_ex_small,
    contig_filter_args = chain == 'TRA' & length > 500, tie_break_keys = 'umis',
    contig_fields = c('chain', 'length'))
    ccdb_umi$cluster_tbl %>% dplyr::select(chain, length) %>% summary()

[Package CellaRepertorium version 1.2.0 Index]