R: Correct allele calls based on a personalized genotype

reassignAlleles {tigger} | R Documentation

## Correct allele calls based on a personalized genotype

### Description

`reassignAlleles` uses a subject-specific genotype to correct correct preliminary allele assignments of a set of sequences derived from a single subject.

### Usage

    reassignAlleles(
      data,
      genotype_db,
      v_call = "v_call",
      seq = "sequence_alignment",
      method = "hamming",
      path = NA,
      keep_gene = c("gene", "family", "repertoire")
    )

### Arguments

`data` | `data.frame` containing V allele calls from a single subject and the sample IMGT-gapped V(D)J sequences under `seq`.
`genotype_db` | vector of named nucleotide germline sequences matching the calls detailed in `allele_calls` and personalized to the subject
`v_call` | name of the column in `data` with V allele calls. Default is `v_call`.
`seq` | name of the column in `data` with the aligned, IMGT-numbered, V(D)J nucleotide sequence. Default is SEQUENCE_IMGT
`method` | method to use when realigning sequences to the genotype_db sequences. Currently, only `"hammming"` (for Hamming distance) is implemented.
`path` | directory containing the tool used in the realignment method, if needed. Hamming distance does not require a path to a tool.
`keep_gene` | string indicating if the gene (`"gene"`), family (`"family"`) or complete repertoire (`"repertoire"`) assignments should be performed. Use of `"gene"` increases speed by minimizing required number of alignments, as gene level assignments will be maintained when possible.

### Details

In order to save time, initial gene assignments are preserved and the allele calls are chosen from among those provided in `genotype_db`, based on a simple alignment to the sample sequence.

### Value

A modifed input `data.frame` containing the best allele call from among the sequences listed in `genotype_db` in the `v_call_genotyped` column.

### Examples

    # Extract the database sequences that correspond to the genotype
    genotype_db <- genotypeFasta(SampleGenotype, SampleGermlineIGHV, novel=SampleNovel)

    # Use the personlized genotype to determine corrected allele assignments
    output_db <- reassignAlleles(AIRRDb, genotype_db, v_call="v_call",
                                 seq="sequence_alignment")

[Package tigger version 1.0.0 Index]