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")

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¶

### Not run:
asc_archive <- recentAlleleClusters(doi="10.5281/zenodo.7401239", get_file = TRUE)

Files will be downloaded to tmp directory: /tmp/Rtmpn83kLadoi supplied is not an ‘all versions doi’ for viewing all of the archive records change the doi to:10.5281/zenodo.7401189

# 
# allele_cluster_table <- extractASCTable(archive_file = asc_archive)
# 
# # loading TIgGER AIRR-seq b cell data
# data <- tigger::AIRRDb
# 
# asc_data <- assignAlleleClusters(data, allele_cluster_table)