kmeRs_twoSeqSim: kmeRs_twoSeqSim

In kmeRs: K-Mers Similarity Score Matrix and HeatMap

kmeRs_twoSeqSim

Description

Supporting func to kmeRs_show_alignment

Usage

kmeRs_twoSeqSim(
  kmer_A,
  kmer_B,
  seq.type = "AA",
  submat = ifelse(test = (match.arg(toupper(seq.type), c("DNA", "AA")) == "AA"), yes =
    "BLOSUM62", no = NA),
  na.match = ifelse(is.na(submat), yes = 2, no = NA),
  na.mismatch = ifelse(is.na(submat), yes = -3, no = NA),
  align.type = "global",
  verbose = TRUE,
  ...
)

Arguments

kmer_A	given k-mer A
kmer_B	given k-mer B
seq.type	type of sequence in question, either 'DNA' or 'AA' (default)
submat	substitution matrix version, defaults to 'BLOSUM62'; other choices include 'BLOSUM45', 'BLOSUM50', 'BLOSUM62', 'BLOSUM80', 'BLOSUM100', 'PAM30', 'PAM40', 'PAM70', 'PAM120' and 'PAM250'; this parameter is ignored if na.match and na.mismatch are specified
na.match	for DNA sequences, what should the score for exact match be?
na.mismatch	for DNA sequences, what should the score for mismatches be?
align.type	"global" or "local"
verbose	= TRUE
...	other parameters, e.g. gap opening/extension penalties (gapOpening, gapExtension) for generating a DNA base substitution matrix

kmeRs documentation built on Sept. 11, 2024, 6:52 p.m.