piglet (version 1.2.0)

assignAlleleClusters: 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",
  from_col = "imgt_allele",
  to_col = "new_allele"
)

Value

A modified input data.frame with the new assigned

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

from_col

name of the column in alleleClusterTable to use as the source for the dictionary. Default is imgt_allele

to_col

name of the column in alleleClusterTable to use as the target for the dictionary. Default is new_allele

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)