Input format¶
RAbHIT works on pre-processed antibody (or TRB) repertoire sequencing data with heterozygosity in at least one gene, plus a database of germline gene sequences.
Repertoire data¶
A data.frame in AIRR format, where each row is a unique
observation. The required columns are:
| Column | Description |
|---|---|
subject |
Subject identifier |
v_call |
(Comma-separated) name(s) of the nearest V allele(s), IMGT format |
d_call |
(Comma-separated) name(s) of the nearest D allele(s), IMGT format |
j_call |
(Comma-separated) name(s) of the nearest J allele(s), IMGT format |
Note
Allele names are expected in IMGT nomenclature (GENE*ALLELE, e.g. IGHV1-2*01). Support for
PIgLET allele-similarity-cluster (ASC) names and OGRDB reference sets is provided via integration
with the piglet package.
Germline database¶
A named character vector of IMGT-gapped germline nucleotide sequences, where names are the IMGT allele
calls (e.g. IGHV1-2*01). RAbHIT bundles reference databases for the supported chains:
| Object | Segment |
|---|---|
HVGERM, HDGERM, HJGERM |
IGH V / D / J |
KVGERM, KJGERM |
IGK V / J |
LVGERM, LJGERM |
IGL V / J |
Load them with data(HVGERM, HDGERM, HJGERM). If you do not pass toHap_GERM, RAbHIT selects the
appropriate bundled germline for the requested chain.
Example data¶
The package ships an example repertoire (samples_db) and a pre-computed haplotype result
(samplesHaplotype) used throughout the Tutorial: