airrClone-class - S4 class defining a clone in Dowser
Description¶
airrClone
defines a common data structure for perform lineage recontruction
from AIRR data, based heavily on alakazam::ChangeoClone.
Slots¶
data
- data.frame containing sequences and annotations. Contains the
columns
sequence_id
andsequence
, as well as any additional sequence-specific annotation columns clone
- string defining the clone identifier
germline
- string containing the heavy chain germline sequence for the clone
lgermline
- string containing the light chain germline sequence for the clone
hlgermline
- string containing the combined germline sequence for the clone
v_gene
- string defining the V segment gene call
j_gene
- string defining the J segment gene call
junc_len
- numeric junction length (nucleotide count)
locus
- index showing which locus represented at each site
region
- index showing FWR/CDR region for each site
phylo_seq
- sequence column used for phylogenetic tree building
numbers
- index (usually IMGT) number of each site in
phylo_seq
See also¶
See formatClones for use.