assignAlleleClusters: Assign allele similarity clusters

In piglet: Program for Inferring Immunoglobulin Allele Similarity Clusters and Genotypes

Assign allele similarity clusters

Description

assignAlleleClusters uses the allele clusters annotation to change the preliminary allele assignments to the new annotations before inferring a genotype.

Usage

assignAlleleClusters(data, alleleClusterTable, v_call = "v_call")

Arguments

data	data.frame in AIRR format, containing V allele calls from a single subject and the sample IMGT-gapped V(D)J sequences under seq.
alleleClusterTable	A data.frame of the allele clusters new annotations relative to the original reference set. See details.
v_call	name of the V allele call column. Default is v_call

Value

A modified input data.frame with the new assigned

Examples

# preferably obtain the latest ASC cluster table
# asc_archive <- recentAlleleClusters(doi="10.5281/zenodo.7429773", get_file = TRUE)

# allele_cluster_table <- extractASCTable(archive_file = asc_archive)

# example allele similarity cluster table
data(allele_cluster_table)

# loading TIgGER AIRR-seq b cell data
data <- tigger::AIRRDb

asc_data <- assignAlleleClusters(data, allele_cluster_table)

piglet documentation built on April 12, 2025, 1:27 a.m.