R: Example Change-O database

ExampleDbChangeo {alakazam}

R Documentation

Example Change-O database

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

ExampleDbChangeo

A data.frame with the following Change-O style columns:

SEQUENCE_ID: Sequence identifier
SEQUENCE_IMGT: IMGT-gapped observed sequence.
GERMLINE_IMGT_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.
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.
SAMPLE: Sample identifier. Time in relation to vaccination.
ISOTYPE: Isotype assignment.
DUPCOUNT: Copy count (number of duplicates) of the sequence.
CLONE: Change-O assignment clonal group identifier.

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.