R: Use 'cdhit()' to cluster a 'ContigCellDB()'

cdhit_ccdb {CellaRepertorium}

R Documentation

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

Description

See https://github.com/weizhongli/cdhit/wiki/3.-User's-Guide#CDHIT for details on other potential arguments to .... These will override any default values.

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 `G` 1 for global alignment, 0 for local. If doubt, pick global.

Value

ContigCellDB()

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 1.4.0 Index]