R: Example AIRR database

ExampleDb {alakazam}

R Documentation

Example AIRR database

A small example database subset from Laserson and Vigneault et al, 2014.

ExampleDb

A data.frame with the following AIRR style columns:

sequence_id: Sequence identifier
sequence_alignment: IMGT-gapped observed sequence.
germline_alignment: IMGT-gapped germline sequence.
germline_alignment_d_mask: IMGT-gapped germline sequence with N, P and D regions masked.
v_call: V region allele assignments.
v_call_genotyped: TIgGER corrected V region allele assignment.
d_call: D region allele assignments.
j_call: J region allele assignments.
c_call: Isotype (C region) assignment.
junction: Junction region sequence.
junction_length: Length of the junction region in nucleotides.
np1_length: Combined length of the N and P regions proximal to the V region.
np2_length: Combined length of the N and P regions proximal to the J region.
duplicate_count: Copy count (number of duplicates) of the sequence.
clone_id: Change-O assignment clonal group identifier.
sample_id: Sample identifier. Time in relation to vaccination.

Laserson U and Vigneault F, et al. High-resolution antibody dynamics of vaccine-induced immune responses. Proc Natl Acad Sci USA. 2014 111:4928-33.