R: Example Change-O database

ExampleDb {alakazam} | R Documentation

## 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

[Package alakazam version 0.3.0 Index]