airrClone-class {dowser} | R Documentation |
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 columnsclone
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.