cdhit_ccdb {CellaRepertorium} | R Documentation |
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 1.0.0
Index]