ExampleDb - Example Change-O database

Description

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

Usage

ExampleDb

Format

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.

References

  1. 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.

See also

ExampleTrees