ExampleDb - Example database

Description

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

Usage

ExampleDb

Format

A data.frame with the following 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.
  • junction: Junction region sequence.
  • junction_length: Length of the junction region in nucleotides.
  • np1_length: Number of nucleotides between V and D segments
  • np2_length: Number of nucleotides between D and J segments
  • sample_id: Sample identifier
  • c_call: C region assignment.
  • duplicate_count: Copy number of the sequence
  • locus: Locus of the receptor

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.