airrClone-class {dowser}

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 and sequence, 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.