ExampleDb: Example database

In scoper: Spectral Clustering-Based Method for Identifying B Cell Clones

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.

scoper documentation built on Oct. 6, 2023, 5:09 p.m.