fine_clustering {CellaRepertorium} | R Documentation

## Perform additional clustering of sequences within groups

### Description

Perform additional clustering of sequences within groups

### Usage

    fine_clustering(
      ccdb,
      sequence_key,
      type,
      max_affinity = NULL,
      keep_clustering_details = FALSE,
      ...
    )

### Arguments

`ccdb` | A `ContigCellDB()` object
`sequence_key` | `character` naming column in `contig_tbl` with sequence
`type` | 'AA' or 'DNA'
`max_affinity` | `numeric` naming the maximal affinity for the sparse affinity matrix that is constructed. Not currently used.
`keep_clustering_details` | `logical` – should output of `fine_cluster_seqs` be kept as a list column
`...` | Arguments passed on to `fine_cluster_seqs` `big_memory_brute` attempt to cluster more than 4000 sequences? Clustering is quadratic, so this will take a long time and might exhaust memory `method` one of 'substitutionMatrix' or 'levenshtein' `substitution_matrix` a character vector naming a substitution matrix available in Biostrings, or a substitution matrix itself

### Value

`ContigCellDB()` object with updated `contig_tbl` and `cluster_tbl`

### 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 1.4.0 Index]