kmeRs_show_alignment {kmeRs}

Calculate and Show Alignment Between Two Compared K-mers

Description

The kmeRs_show_alignment function aligns and shows calculated alignment between two DNA or RNA sequences

Usage

kmeRs_show_alignment(
  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

Value

alignment is returned as a data frame

Examples

# Example DNA alignment with gap opening and extension penalties of 1 and 0
# with default base match/mismatch values

kmeRs_show_alignment(kmer_A = "AAATTTCCCGGG", kmer_B = "TCACCC",
    seq.type = "DNA", gapOpening = 1, gapExtension = 0)