piglet (version 1.2.0)

igDistance: Germline set alleles distance

Description

Calculates the distance between pairs of alleles based on their aligned germline sequences. Supports multiple distance methods for different segment types.

Usage

igDistance(
  germline_set,
  AA = FALSE,
  method = c("decipher", "hamming", "lv"),
  trim_3prime = NULL,
  return_type = c("matrix", "dist"),
  quiet = TRUE
)

Value

A matrix or dist object of the computed distances between allele pairs.

Arguments

germline_set

A character vector of aligned allele sequences. See details for curating options.

AA

Logical (FALSE by default). If TRUE, calculate the distance based on amino acid sequences.

method

Distance calculation method. One of:

• "decipher": Uses DECIPHER::DistanceMatrix (requires aligned sequences, best for V segments)

• "hamming": Hamming distance (requires equal length, sequences padded if needed)

• "lv": Levenshtein distance (handles variable length, good for D/J segments)

trim_3prime

Optional position to trim sequences from 3' end before distance calculation

return_type

One of "matrix" (default) or "dist" to return a dist object

quiet

Logical (TRUE by default). Suppress informative messages

Details

The aligned IMGT IGHV allele germline set can be downloaded from the IMGT site https://www.imgt.org/ under the section genedb.

For V segments, the "decipher" method is recommended as it handles alignment gaps properly. For D and J segments which may have variable lengths, the "lv" (Levenshtein) method is appropriate.

See Also

ighvDistance for backward compatibility wrapper

Examples

data(HVGERM)
# Using DECIPHER method (default, for V segments)
d1 <- igDistance(HVGERM[1:10], method = "decipher")

# Using Hamming distance
d2 <- igDistance(HVGERM[1:10], method = "hamming")

# Using Levenshtein distance (good for D/J segments)
d3 <- igDistance(HVGERM[1:10], method = "lv")