piglet (version 1.0.7)

allele_diff: 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
)

Value

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

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.

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)

}