Get Sequence Statistics

Analyzes sequences to provide statistics about length, composition, and optionally comparison metrics (reference similarity, pairwise identity), k-mer entropy, and data-quality flags.

Usage

getSequenceStats(
  sequences,
  type = c("PROT", "NUC"),
  ref = NULL,
  k = 2L,
  ignore_chars = c("*", "-", " "),
  compute_pairs = FALSE,
  warn_invalid = TRUE
)

Arguments

sequences

Named list (or named character vector) of sequences (e.g., output from batchGetSequences). Names should be allele IDs.

type

Type of sequences: "PROT" (amino acids) or "NUC" (nucleotides).

ref

Optional reference for comparison; either the *name* of one sequence in `sequences` or a raw sequence string of the same `type`.

k

Integer k for k-mer Shannon entropy (default 2).

ignore_chars

Characters to ignore when computing counts/identity (default c("*", "-", " ")). Useful for protein stop symbols or gaps.

compute_pairs

Logical; if TRUE, also compute a pairwise percent identity matrix (alignment-free, position-wise) and return a list with `stats` and `pairwise_identity`. Default FALSE (returns only `stats`).

warn_invalid

Logical; if TRUE (default), warn when invalid symbols for the chosen `type` are detected.

Value

If `compute_pairs = FALSE` (default): a data.frame with per-sequence stats. If `compute_pairs = TRUE`: a list with elements: - `stats`: per-sequence stats data.frame - `pairwise_identity`: numeric matrix (0..1) of

Examples

alleles <- c("A*01:01", "A*02:01", "B*07:02")
seqs <- batchGetSequences(alleles)
stats <- getSequenceStats(seqs, type = "PROT")