selectNovel: Select rows containing novel alleles

In tigger: Infers Novel Immunoglobulin Alleles from Sequencing Data

Select rows containing novel alleles

Description

selectNovel takes the result from findNovelAlleles and selects only the rows containing unique, novel alleles.

Usage

selectNovel(novel, keep_alleles = FALSE)

Arguments

novel	data.frame of the type returned by findNovelAlleles.
keep_alleles	logical indicating if different alleles leading to the same novel sequence should be kept. See Details.

Details

If, for instance, subject has in his genome IGHV1-2*02 and a novel allele equally close to IGHV1-2*02 and IGHV1-2*05, the novel allele may be detected by analyzing sequences that best align to either of these alleles. If keep_alleles is TRUE, both polymorphic allele calls will be retained. In the case that multiple mutation ranges are checked for the same allele, only one mutation range will be kept in the output.

Value

A data.frame containing only unique, novel alleles (if any) that were in the input.

Examples

novel <- selectNovel(SampleNovel)

tigger documentation built on Oct. 10, 2023, 5:08 p.m.