codon_diff: Find codon differences between sequences

In ryanmcnamara4/myPackage: Useful functions for dealing with biological data/sequences

Description

Function takes a baseline sequence and any number of sequences to compare to and determines the number or the positions of the codon (3 characters) differences.

Usage

codon_diff(
  baseline_seq,
  compare_seqs,
  diff_type = c("synonymous", "non-synonymous", "all"),
  output = c("num", "position"),
  seq_type = c("DNA", "RNA"),
  ignore_case = TRUE
)

Arguments

baseline_seq	Character vector of length one that all other sequences are being compared to.
compare_seqs	Character vector of any length that will be compared to the baseline sequence.
diff_type	Either "synonymous", "non-synonymous", or "all". "all" : find all the codon differences "non-synonymous" : find all of the non-synonymous codon differences "synonymous" : find all of the synonymous codon differences
output	Either "num" (return the number of differences) or "position" (return the positions of the differences).
seq_type	Character value of "DNA" or "RNA" describing whether the sequences use "T" or "U".
ignore_case	Logical value (TRUE / FALSE) designating whether the function should ignore case. Defaults to TRUE.

Value

Either a list of numeric vectors describing the positions of the differences or a numeric vector of the number of differences.

Examples

codon_diff('AGTGGG', 'CGTGAG', output = 'num', diff_type = 'all', seq_type = 'DNA')

seq1 = 'ACTGACTGG'
seq2 = c('ACGGGCCGG', 'ACTGACTGG', 'GCTCAGTGG')
codon_diff(seq1, seq2, output = 'num', diff_type = 'synonymous',
    seq_type = 'DNA', ignore_case = TRUE)
codon_diff(seq1, seq2, output = 'position', diff_type = 'non-synonymous',
    seq_type = 'DNA', ignore_case = FALSE)

seq1 = 'ACUGACUGG'
seq2 = c('ACGGGCCGG', 'ACUGACUGG', 'GCUCAGUGG')
codon_diff(seq1, seq2, output = 'num', diff_type = 'synonymous',
    seq_type = 'RNA', ignore_case = TRUE)
codon_diff(seq1, seq2, output = 'position', diff_type = 'non-synonymous',
    seq_type = 'RNA', ignore_case = FALSE)

## Not run: 
codon_diff(seq1, seq2)
codon_diff('AGTCGA', 'TTA')

## End(Not run)

ryanmcnamara4/myPackage documentation built on Dec. 22, 2021, 8:18 p.m.