inferGenotypeAllele

inferGenotypeAllele - Allele similarity cluster based genotype inference

Description¶

inferGenotypeAllele infer an individual’s genotype based on the allele-base method. The method utilize the allele specific threshold to determine the presence of an allele in the genotype. More specifically, the absolute frequency of each allele is calculated and checked against the threshold.

Usage¶

inferGenotypeAllele(
data,
alleleClusterTable,
v_call = "v_call",
single_assignment = FALSE,
germline_db = NA,
find_unmutated = FALSE,
seq = "sequence_alignment"
)

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 similarity clusters thresholds.
v_call: name of the V allele call column. Default is v_call
single_assignment: if TRUE, the method only considers sequence with single assignment for the genotype inference.
germline_db: named vector of sequences containing the germline sequences named in V allele calls and the alleleClusterTable. Only required if find_unmutated is TRUE.
find_unmutated: if TRUE, use germline_db to find which samples are unmutated. Not needed if V allele calls only represent unmutated samples.
seq: name of the column in data with the aligned, IMGT-numbered, V(D)J nucleotide sequence. Default is sequence_alignment.

Value¶

A a data.frame with the inferred V genotype. The table contains the following columns:

gene	alleles	imgt_alleles	counts	absolute_fraction	absolute_threshold	genotyped_alleles
genotype_imgt_alleles	allele cluster	the present alleles	the imgt nomenclature	the number of reads	the absolute fraction	the population driven allele
the alleles which	the imgt nomenclature		in the repertoire	of the alleles	for each alleles	of the alleles
thresholds for genotype presence	entered the genotype	of the alleles	gene	alleles	imgt_alleles	counts

Details¶

In naive repertoires, allele calls where more than one assignment is assigned is rare. Hence, in case the data represents the naive repertoire of a subject it is recommended to use the find_unmutated=TRUE option, to remove mutated sequences. For non-naive population, the allele calls in cases of multiple assignment are treated as belonging to all groups.

Examples¶

### Not run:
# loading TIgGER AIRR-seq b cell data
# data <- tigger::AIRRDb
# 
# # getting the archive
# asc_archive <- recentAlleleClusters(doi="10.5281/zenodo.7401239", get_file = TRUE)
# 
# # extracting the allele cluster table
# allele_cluster_table <- extractASCTable(archive_file = asc_archive)
# 
# data(HVGERM)
# 
# # reforming the germline set
# asc_germline <- germlineASC(allele_cluster_table, germline = HVGERM)
# 
# # assigning the ASC alleles
# asc_data <- assignAlleleClusters(data, allele_cluster_table)
# 
# # inferring the genotype
# asc_genotype <- inferGenotypeAllele(asc_data,
# alleleClusterTable = allele_cluster_table,
# germline_db = asc_germline, find_unmutated=T)