cdhit_ccdb {CellaRepertorium} | R Documentation

## Use `cdhit()` to cluster a `ContigCellDB()`

### Description

Use `cdhit()` to cluster a `ContigCellDB()`

### Usage

    cdhit_ccdb(
      ccdb,
      sequence_key,
      type = c("DNA", "AA"),
      cluster_pk = "cluster_idx",
      ...
    )

### Arguments

`ccdb` | An object of class `ContigCellDB()`
`sequence_key` | `character` naming the column in the `contig_tbl` containing the sequence to be clustered
`type` | one of 'DNA' or 'AA'
`cluster_pk` | `character` specifying key, and name for the clustering.
`...` | Arguments passed on to `cdhit` `identity` minimum proportion identity `kmerSize` word size. If NULL, it will be chosen automatically based on the identity. You may need to lower it below 5 for AAseq with identity less than .7. `min_length` Minimum length for sequences to be clustered. An error if something smaller is passed. `s` fraction of shorter sequence covered by alignment. `showProgress` show a status bar

### Value

`ContigCellDB()`

### See Also

`cdhit()`

### Examples

    data(ccdb_ex)
    res = cdhit_ccdb(ccdb_ex, 'cdr3_nt', type = 'DNA',
    cluster_name = 'DNA97', identity = .965, min_length = 12, G = 1)
    res$cluster_tbl
    res$contig_tbl
    res$cluster_pk

[Package CellaRepertorium version 1.2.0 Index]