rank_prevalence_ccdb {CellaRepertorium} | R Documentation |
cluster_pk
, which is added as the prevalence
fieldRank contigs, per cell, by experiment-wide prevalence of cluster_pk
, which is added as the prevalence
field
rank_prevalence_ccdb( ccdb, contig_filter_args = TRUE, tie_break_keys = c("umis", "reads") ) rank_chain_ccdb( ccdb, contig_filter_args = TRUE, tie_break_keys = c("umis", "reads"), chain_key = "chain", contig_fields = tie_break_keys, chain_levels = c("IGL", "IGK", "TRA", "TRB", "IGH") )
ccdb |
|
contig_filter_args |
an expression passed to |
tie_break_keys |
(optional) |
chain_key |
|
contig_fields |
Optional fields from |
chain_levels |
an optional |
ContigCellDB
with modified contig_tbl
rank_chain_ccdb
: return a canonical contig by chain type, with TRB/IGH returned first. By default, ties are broken by umis and reads.
data(ccdb_ex) ccdb_ex = cluster_germline(ccdb_ex) rank_prev = rank_prevalence_ccdb(ccdb_ex) rank_prev$contig_tbl rank_chain = rank_chain_ccdb(ccdb_ex) rank_chain$contig_tbl