allele_diff: Alleles nucleotide position difference

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

Alleles nucleotide position difference

Description

Compare the sequences of two alleles (reference and sample alleles) and returns the differential nucleotide positions of the sample allele.

Usage

allele_diff(
  reference_allele,
  sample_allele,
  position_threshold = 0,
  snps = TRUE
)

Arguments

reference_allele	The nucleotide sequence of the reference allele, character object.
sample_allele	The nucleotide sequence of the sample allele, character object.
position_threshold	A position from which to check for differential positions. If zero checks all position. Default to zero.
snps	If to return the SNP with the position (e.g., A2G where A is for the reference and G is for the sample.). If false returns just the positions. Default to True

Details

The function utilizes c++ script to optimize the run time for large comparisons.

Value

A character vector of the differential nucleotide positions of the sample allele.

Examples

{
reference_allele = "AAGG"
sample_allele = "ATGA"

# setting position_threshold = 0 will return all differences
diff <- allele_diff(reference_allele, sample_allele)
# "A2T", "G4A"
print(diff)

# setting position_threshold = 3 will return the differences from position three onward
diff <- allele_diff(reference_allele, sample_allele, position_threshold = 3)
# "G4A"
print(diff)

# setting snps = FALSE will return the differences as indices
diff <- allele_diff(reference_allele, sample_allele, snps = FALSE)
# 2, 4
print(diff)

}

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