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Quantify Amino Acid Mismatches With Charge/Polarity Awareness (base R)

Source: R/quantifyMismatch.R
quantifyMismatch.Rd

Compares two amino acid sequences (same length) and quantifies mismatches. Each mismatch is annotated for whether it changes residue charge and/or polarity. Users can filter which mismatches to count based on these properties.

Usage

quantifyMismatch(
  sequence1,
  sequence2,
  filter_charge = NULL,
  filter_polarity = NULL,
  return = c("count", "detail"),
  na_action = c("exclude", "error", "count"),
  type = c("global", "local", "overlap"),
  substitutionMatrix = "BLOSUM80",
  gapOpening = 10,
  gapExtension = 1,
  count_gaps = TRUE
)

Arguments

sequence1, sequence2

Character strings of equal length (AAs).

filter_charge

NULL/TRUE/FALSE - `NULL` (default): ignore charge when filtering (i.e., do not filter). - `TRUE`: count only mismatches that change charge. - `FALSE`: count only mismatches that do *not* change charge.

filter_polarity

NULL/TRUE/FALSE. - `NULL` (default): ignore polarity when filtering. - `TRUE`: count only mismatches that change polarity. - `FALSE`: count only mismatches that do *not* change polarity.

return

What to return: one of "count" (default) or "detail"

na_action

One of "exclude" (default), "error", "count". Controls handling of unknown residues (e.g., X, *, -).

type

Character string. The type of alignment to perform. Defaults to `"global"` but allows for `"local"` and `"overlap"`-based alignments of the sequences.

substitutionMatrix

Character string or numeric matrix. Substitution scoring matrix used during sequence alignment. Defaults to `"BLOSUM80"`, which provides a conservative amino acid similarity scheme suitable for closely related protein sequences.

gapOpening

Numeric scalar. Penalty score applied when initiating a new gap during alignment. Higher values discourage insertion/deletion events and yield more contiguous alignments. Default is `10`.

gapExtension

Numeric scalar. Penalty score applied when extending an existing gap. Smaller values permit longer continuous gaps, while larger values favor shorter gaps. Default is `1`.

count_gaps

Logical (default `TRUE`). If `TRUE`, positions where one sequence contains a gap (`-`) and the other contains an amino acid are treated as mismatches and included in the mismatch count.

Value

- If return = "count": integer (count after filters). - If return = "detail": a table with columns: position, ref, alt, is_mismatch, charge_ref, charge_alt, charge_change, polarity_ref, polarity_alt, polarity_change, counted.

Examples

seq1 <- "YFAMYGEKVAHTHVDTLYVRYHY"
seq2 <- "YFDMYGEKVAHTHVDTLYVRFHY"

# Numerical quantification of mismatches
quantifyMismatch(seq1, seq2)
#> [1] 2

# Count only mismatches that change charge
quantifyMismatch(seq1, seq2, filter_charge = TRUE)
#> [1] 1

# Count only mismatches that change polarity
quantifyMismatch(seq1, seq2, filter_polarity = TRUE)
#> [1] 2

# Count mismatches that change charge AND polarity
quantifyMismatch(seq1, seq2, filter_charge = TRUE, filter_polarity = TRUE)
#> [1] 1