ExampleDbChangeo: Example Change-O database

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Example Change-O database

Description

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

Usage

ExampleDbChangeo

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

ExampleDb ExampleTrees

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