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

In CellaRepertorium: Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)

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

CellaRepertorium documentation built on Nov. 8, 2020, 7:48 p.m.