inferGenotypeAllele_asc: Allele similarity cluster based genotype inference Testing function

Description

inferGenotypeAllele_asc 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_asc(
  data,
  alleleClusterTable,
  v_call = "v_call",
  single_assignment = FALSE,
  germline_db = NA,
  find_unmutated = FALSE,
  seq = "sequence_alignment",
  confidence_level = NULL,
  default_allele_threshold = 1e-04
)

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

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.
confidence_level: The confidence level on which to filter the inferred genotype alleles. Default is NULL, meaning filtering only based on allele threshold.
default_allele_threshold: The default allele threshold for the genotype inference, in case the allele threshold is not in the alleleClusterTable. Default is 1e-04.

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

Run this code



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

# 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)

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 = asc_data,
alleleClusterTable = allele_cluster_table,
germline_db = asc_germline, find_unmutated=TRUE)