kmeRs_show_alignment: Calculate and Show Alignment Between Two Compared K-mers

In kmeRs: K-Mers Similarity Score Matrix and HeatMap

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)
    

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