ExampleDb: Example AIRR database

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Example AIRR database

Description

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

Usage

ExampleDb

Format

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.

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

ExampleDbChangeo ExampleTrees

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.